inDAGO

A GUI for Dual and Bulk RNA-Sequencing Analysis

v1.0.3 · Oct 21, 2025 · GPL (>= 3)

Description

A 'shiny' app that supports both dual and bulk RNA-seq, with the dual RNA-seq functionality offering the flexibility to perform either a sequential approach (where reads are mapped separately to each genome) or a combined approach (where reads are aligned to a single merged genome). The user-friendly interface automates the analysis process, providing step-by-step guidance, making it easy for users to navigate between different analysis steps, and download intermediate results and publication-ready plots.

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CRAN Check Status

1 ERROR

2 NOTE

11 OK

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	907.6s
r-devel-linux-x86_64-debian-gcc	OK	248.1s
r-devel-linux-x86_64-fedora-clang	OK	771.3s
r-devel-linux-x86_64-fedora-gcc	NOTE	956.2s
r-devel-macos-arm64	OK	101s
r-devel-windows-x86_64	OK	364s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	NOTE	611s
r-oldrel-windows-x86_64	OK	475s
r-patched-linux-x86_64	OK	338.2s
r-release-linux-x86_64	OK	335.6s
r-release-macos-arm64	OK
r-release-macos-x86_64	OK	492s
r-release-windows-x86_64	OK	361s

Check details (14 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

tests

  Running ‘testthat.R’ [11m/15m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > # library("testthat")
  > # library("inDAGO")
  > 
  > testthat::test_check("inDAGO")
  Loading required package: inDAGO
  The following packages are not installed: ShortRead, rtracklayer, Rsamtools, HTSFilter, Biostrings.
  To enable all the features of inDAGO, install with:
    if (!requireNamespace('BiocManager', quietly=TRUE))
      install.packages('BiocManager')
    BiocManager::install(c("ShortRead", "rtracklayer", "Rsamtools", "HTSFilter", "Biostrings"))
  
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///srv/R/Repositories/CRAN
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-04 r89535)
  Installing package(s) 'BiocVersion', 'ShortRead'
  also installing the dependencies 'formatR', 'abind', 'SparseArray', 'lambda.r', 'futile.options', 'MatrixGenerics', 'S4Arrays', 'DelayedArray', 'deldir', 'RcppEigen', 'futile.logger', 'snow', 'bitops', 'SummarizedExperiment', 'cigarillo', 'png', 'jpeg', 'interp', 'BiocParallel', 'Biostrings', 'Rsamtools', 'GenomicAlignments', 'Biobase', 'Seqinfo', 'GenomicRanges', 'pwalign', 'hwriter', 'latticeExtra', 'Rhtslib'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/MatrixGenerics_1.23.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/S4Arrays_1.11.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/cigarillo_1.1.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocParallel_1.45.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicAlignments_1.47.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biobase_2.71.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Seqinfo_1.1.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicRanges_1.63.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/pwalign_1.7.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rhtslib_3.7.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocVersion_3.23.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/ShortRead_1.69.2.tar.gz'
  * installing *source* package ‘formatR’ ...
  ** this is package ‘formatR’ version ‘1.14’
  ** package ‘formatR’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** 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
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  * DONE (formatR)
  * installing *source* package ‘abind’ ...
  ** this is package ‘abind’ version ‘1.4-8’
  ** package ‘abind’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (abind)
  * installing *source* package ‘futile.options’ ...
  ** this is package ‘futile.options’ version ‘1.0.1’
  ** package ‘futile.options’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (futile.options)
  * installing *source* package ‘MatrixGenerics’ ...
  ** this is package ‘MatrixGenerics’ version ‘1.23.0’
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’
  Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (MatrixGenerics)
  * installing *source* package ‘deldir’ ...
  ** this is package ‘deldir’ version ‘2.0-4’
  ** package ‘deldir’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  using Fortran compiler: ‘Debian flang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpkGOTa8/R.INSTALL12736851d8aed0/deldir/src'
  flang-21  -fpic  -g -O2 -c  acchk.f90 -o acchk.o
  flang-21  -fpic  -g -O2 -c  addpt.f90 -o addpt.o
  flang-21  -fpic  -g -O2 -c  adjchk.f90 -o adjchk.o
  flang-21  -fpic  -g -O2 -c  binsrt.f90 -o binsrt.o
  flang-21  -fpic  -g -O2 -c  circen.f90 -o circen.o
  flang-21  -fpic  -g -O2 -c  cross.f90 -o cross.o
  flang-21  -fpic  -g -O2 -c  delet.f90 -o delet.o
  flang-21  -fpic  -g -O2 -c  delet1.f90 -o delet1.o
  flang-21  -fpic  -g -O2 -c  delout.f90 -o delout.o
  flang-21  -fpic  -g -O2 -c  delseg.f90 -o delseg.o
  flang-21  -fpic  -g -O2 -c  dirout.f90 -o dirout.o
  flang-21  -fpic  -g -O2 -c  dirseg.f90 -o dirseg.o
  flang-21  -fpic  -g -O2 -c  dldins.f90 -o dldins.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
  flang-21  -fpic  -g -O2 -c  initad.f90 -o initad.o
  flang-21  -fpic  -g -O2 -c  insrt.f90 -o insrt.o
  flang-21  -fpic  -g -O2 -c  insrt1.f90 -o insrt1.o
  flang-21  -fpic  -g -O2 -c  intri.f90 -o intri.o
  flang-21  -fpic  -g -O2 -c  locn.f90 -o locn.o
  flang-21  -fpic  -g -O2 -c  master.f90 -o master.o
  flang-21  -fpic  -g -O2 -c  mnnd.f90 -o mnnd.o
  flang-21  -fpic  -g -O2 -c  pred.f90 -o pred.o
  flang-21  -fpic  -g -O2 -c  qtest.f90 -o qtest.o
  flang-21  -fpic  -g -O2 -c  qtest1.f90 -o qtest1.o
  flang-21  -fpic  -g -O2 -c  stoke.f90 -o stoke.o
  flang-21  -fpic  -g -O2 -c  succ.f90 -o succ.o
  flang-21  -fpic  -g -O2 -c  swap.f90 -o swap.o
  flang-21  -fpic  -g -O2 -c  testeq.f90 -o testeq.o
  flang-21  -fpic  -g -O2 -c  triar.f90 -o triar.o
  flang-21  -fpic  -g -O2 -c  trifnd.f90 -o trifnd.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout.o delseg.o dirout.o dirseg.o dldins.o init.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpkGOTa8/R.INSTALL12736851d8aed0/deldir/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpkGOTa8/R.INSTALL12736851d8aed0/deldir/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpkGOTa8/R.INSTALL12736851d8aed0/deldir/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-deldir/00new/deldir/libs
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (deldir)
  * installing *source* package ‘RcppEigen’ ...
  ** this is package ‘RcppEigen’ version ‘0.3.4.0.2’
  ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNwslgw/R.INSTALL12867b57f3a89f/RcppEigen/src'
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O3 -Wall -pedantic   -c RcppEigen.cpp -o RcppEigen.o
  In file included from RcppEigen.cpp:22:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:29:
  In file included from ../inst/include/Eigen/Sparse:26:
  In file included from ../inst/include/Eigen/SparseCore:61:
  ../inst/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from RcppEigen.cpp:22:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:29:
  In file included from ../inst/include/Eigen/Sparse:29:
  In file included from ../inst/include/Eigen/SparseLU:35:
  ../inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  ../inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from RcppEigen.cpp:22:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:31:
  In file included from ../inst/include/unsupported/Eigen/IterativeSolvers:46:
  ../inst/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from RcppEigen.cpp:22:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:37:
  In file included from ../inst/include/unsupported/Eigen/SparseExtra:45:
  ../inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O3 -Wall -pedantic   -c RcppExports.cpp -o RcppExports.o
  In file included from RcppExports.cpp:4:
  In file included from ./../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:29:
  In file included from ../inst/include/Eigen/Sparse:26:
  In file included from ../inst/include/Eigen/SparseCore:61:
  ../inst/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from RcppExports.cpp:4:
  In file included from ./../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:29:
  In file included from ../inst/include/Eigen/Sparse:29:
  In file included from ../inst/include/Eigen/SparseLU:35:
  ../inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  ../inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from RcppExports.cpp:4:
  In file included from ./../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:31:
  In file included from ../inst/include/unsupported/Eigen/IterativeSolvers:46:
  ../inst/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from RcppExports.cpp:4:
  In file included from ./../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:37:
  In file included from ../inst/include/unsupported/Eigen/SparseExtra:45:
  ../inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I../inst/include -fpic  -g -O3 -Wall -pedantic   -c fastLm.cpp -o fastLm.o
  In file included from fastLm.cpp:23:
  In file included from ./fastLm.h:25:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:29:
  In file included from ../inst/include/Eigen/Sparse:26:
  In file included from ../inst/include/Eigen/SparseCore:61:
  ../inst/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from fastLm.cpp:23:
  In file included from ./fastLm.h:25:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:29:
  In file included from ../inst/include/Eigen/Sparse:29:
  In file included from ../inst/include/Eigen/SparseLU:35:
  ../inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  ../inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from fastLm.cpp:23:
  In file included from ./fastLm.h:25:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:31:
  In file included from ../inst/include/unsupported/Eigen/IterativeSolvers:46:
  ../inst/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from fastLm.cpp:23:
  In file included from ./fastLm.h:25:
  In file included from ../inst/include/RcppEigen.h:25:
  In file included from ../inst/include/RcppEigenForward.h:37:
  In file included from ../inst/include/unsupported/Eigen/SparseExtra:45:
  ../inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNwslgw/R.INSTALL12867b57f3a89f/RcppEigen/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNwslgw/R.INSTALL12867b57f3a89f/RcppEigen/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNwslgw/R.INSTALL12867b57f3a89f/RcppEigen/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-RcppEigen/00new/RcppEigen/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 (RcppEigen)
  * installing *source* package ‘snow’ ...
  ** this is package ‘snow’ version ‘0.4-4’
  ** package ‘snow’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (snow)
  * installing *source* package ‘bitops’ ...
  ** this is package ‘bitops’ version ‘1.0-9’
  ** package ‘bitops’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcK1Vwk/R.INSTALL12e8fdecbcd1/bitops/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c bit-ops.c -o bit-ops.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c cksum.c -o cksum.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o bitops.so bit-ops.o cksum.o init.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcK1Vwk/R.INSTALL12e8fdecbcd1/bitops/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcK1Vwk/R.INSTALL12e8fdecbcd1/bitops/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcK1Vwk/R.INSTALL12e8fdecbcd1/bitops/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-bitops/00new/bitops/libs
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (bitops)
  * installing *source* package ‘png’ ...
  ** this is package ‘png’ version ‘0.1-8’
  ** package ‘png’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpV97awS/R.INSTALL12ee3b36f1603f/png/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   `libpng-config --cflags` -fpic  -g -O3 -Wall -pedantic -c dummy.c -o dummy.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   `libpng-config --cflags` -fpic  -g -O3 -Wall -pedantic -c read.c -o read.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   `libpng-config --cflags` -fpic  -g -O3 -Wall -pedantic -c write.c -o write.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o png.so dummy.o read.o write.o -lpng16 -lz -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpV97awS/R.INSTALL12ee3b36f1603f/png/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpV97awS/R.INSTALL12ee3b36f1603f/png/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpV97awS/R.INSTALL12ee3b36f1603f/png/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-png/00new/png/libs
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (png)
  * installing *source* package ‘jpeg’ ...
  ** this is package ‘jpeg’ version ‘0.1-11’
  ** package ‘jpeg’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpY1cM03/R.INSTALL12f47a7a9e63e8/jpeg/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c read.c -o read.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c reg.c -o reg.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c write.c -o write.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o jpeg.so read.o reg.o write.o -ljpeg -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpY1cM03/R.INSTALL12f47a7a9e63e8/jpeg/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpY1cM03/R.INSTALL12f47a7a9e63e8/jpeg/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpY1cM03/R.INSTALL12f47a7a9e63e8/jpeg/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-jpeg/00new/jpeg/libs
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (jpeg)
  * installing *source* package ‘Biobase’ ...
  ** this is package ‘Biobase’ version ‘2.71.0’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkvnl3I/R.INSTALL12f7de491e23aa/Biobase/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c Rinit.c -o Rinit.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c envir.c -o envir.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c matchpt.c -o matchpt.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c rowMedians.c -o rowMedians.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o Biobase.so Rinit.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkvnl3I/R.INSTALL12f7de491e23aa/Biobase/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpkvnl3I/R.INSTALL12f7de491e23aa/Biobase/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpkvnl3I/R.INSTALL12f7de491e23aa/Biobase/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-Biobase/00new/Biobase/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 (Biobase)
  * installing *source* package ‘Seqinfo’ ...
  ** this is package ‘Seqinfo’ version ‘1.1.0’
  ** using staged installation
  ** 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
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  * DONE (Seqinfo)
  * installing *source* package ‘hwriter’ ...
  ** this is package ‘hwriter’ version ‘1.3.2.1’
  ** package ‘hwriter’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** 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
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  * DONE (hwriter)
  * installing *source* package ‘Rhtslib’ ...
  ** this is package ‘Rhtslib’ version ‘3.7.0’
  ** using non-staged installation via StagedInstall field
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src'
  cd "htslib-1.18" && make -f "Makefile.Rhtslib"
  make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src/htslib-1.18'
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
  echo '#define HTS_VERSION_TEXT "1.18"' > version.h
  printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
  'clang-21 -std=gnu23' \
  '-I/usr/local/include -D_FILE_OFFSET_BITS=64' \
  '-g -O3 -Wall -pedantic -fpic -fvisibility=hidden' \
  '-Wl,-O1 -fvisibility=hidden' \
  '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c
  ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o
  ranlib libhts.a
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kfunc.pico kfunc.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kstring.pico kstring.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bcf_sr_sort.pico bcf_sr_sort.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bgzf.pico bgzf.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o errmod.pico errmod.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o faidx.pico faidx.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o header.pico header.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile.pico hfile.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts.pico hts.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_expr.pico hts_expr.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_os.pico hts_os.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o md5.pico md5.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o multipart.pico multipart.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o probaln.pico probaln.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o realn.pico realn.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o regidx.pico regidx.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o region.pico region.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam.pico sam.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam_mods.pico sam_mods.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o synced_bcf_reader.pico synced_bcf_reader.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf_sweep.pico vcf_sweep.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o tbx.pico tbx.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o textutils.pico textutils.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o thread_pool.pico thread_pool.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf.pico vcf.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcfutils.pico vcfutils.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_codecs.pico cram/cram_codecs.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_decode.pico cram/cram_decode.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_encode.pico cram/cram_encode.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_external.pico cram/cram_external.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_index.pico cram/cram_index.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_io.pico cram/cram_io.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_stats.pico cram/cram_stats.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/mFILE.pico cram/mFILE.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/open_trace_file.pico cram/open_trace_file.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/string_alloc.pico cram/string_alloc.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
  clang-21 -std=gnu23 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_libcurl.pico hfile_libcurl.c
  clang-21 -std=gnu23 -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-O1 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread
  ln -sf libhts.so libhts.so.3
  make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src/htslib-1.18'
  mkdir -p "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/include/htslib"
  cd "htslib-1.18/htslib" && cp * "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/include/htslib"
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Rhtslib.c -o R_init_Rhtslib.o
  mkdir -p "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/usrlib"
  cd "htslib-1.18" && cp libhts.so libhts.a "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/usrlib"
  cd "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o Rhtslib.so R_init_Rhtslib.o /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  mkdir -p "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/testdata/tabix"
  cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/testdata/tabix" 2>/dev/null || true)
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src'
  cd "htslib-1.18" && make -f "Makefile.Rhtslib"
  make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src/htslib-1.18'
  make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src/htslib-1.18'
  mkdir -p "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/include/htslib"
  cd "htslib-1.18/htslib" && cp * "/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/include/htslib"
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/include"  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Rhtslib.c -o R_init_Rhtslib.o
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgQs1rb/R.INSTALL132cc129fd16ef/Rhtslib/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rhtslib/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
  * DONE (Rhtslib)
  * installing *source* package ‘BiocVersion’ ...
  ** this is package ‘BiocVersion’ version ‘3.23.1’
  ** using staged installation
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (BiocVersion)
  * installing *source* package ‘lambda.r’ ...
  ** this is package ‘lambda.r’ version ‘1.2.4’
  ** package ‘lambda.r’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (lambda.r)
  * installing *source* package ‘S4Arrays’ ...
  ** this is package ‘S4Arrays’ version ‘1.11.1’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpolYxLi/R.INSTALL13c385347838d6/S4Arrays/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_S4Arrays.c -o R_init_S4Arrays.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c abind.c -o abind.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c array_selection.c -o array_selection.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c dim_tuning_utils.c -o dim_tuning_utils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c rowsum.c -o rowsum.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpolYxLi/R.INSTALL13c385347838d6/S4Arrays/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpolYxLi/R.INSTALL13c385347838d6/S4Arrays/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpolYxLi/R.INSTALL13c385347838d6/S4Arrays/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-S4Arrays/00new/S4Arrays/libs
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’
  Creating a new generic function for ‘abind’ in package ‘S4Arrays’
  ** 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 (S4Arrays)
  * installing *source* package ‘interp’ ...
  ** this is package ‘interp’ version ‘1.1-6’
  ** package ‘interp’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  using Fortran compiler: ‘Debian flang version 21.1.8 (3+b1)’
  using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT5Of4m/R.INSTALL13ebd2719b480f/interp/src'
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c BiLin.cpp -o BiLin.o
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c RcppExports.cpp -o RcppExports.o
  In file included from RcppExports.cpp:4:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from RcppExports.cpp:4:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from RcppExports.cpp:4:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from RcppExports.cpp:4:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c aSpline.cpp -o aSpline.o
  In file included from aSpline.cpp:7:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from aSpline.cpp:7:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from aSpline.cpp:7:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from aSpline.cpp:7:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  flang-21  -fpic  -g -O2 -c bilinear.f -o bilinear.o
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c circum.cpp -o circum.o
  In file included from circum.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from circum.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from circum.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from circum.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c common.cpp -o common.o
  In file included from common.cpp:1:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from common.cpp:1:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from common.cpp:1:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from common.cpp:1:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c convexHull.cpp -o convexHull.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c interp.cpp -o interp.o
  In file included from interp.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from interp.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from interp.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from interp.cpp:3:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c partDeriv.cpp -o partDeriv.o
  In file included from partDeriv.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from partDeriv.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from partDeriv.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from partDeriv.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c s_hull_pro.cpp -o s_hull_pro.o
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rcpp/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c shullDeltri.cpp -o shullDeltri.o
  In file included from shullDeltri.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:26:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseCore:61:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
        |             ^
  In file included from shullDeltri.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/Sparse:29:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/SparseLU:35:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
     78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        |         ^
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
     79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        |         ^
  In file included from shullDeltri.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:31:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
     72 |                         Index replacements = 0;
        |                               ^
  In file included from shullDeltri.cpp:2:
  In file included from ./interp.h:7:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigen.h:25:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/RcppEigenForward.h:37:
  In file included from /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
  /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    246 |   int count = 0;
        |       ^
  5 warnings generated.
  clang++-21 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o interp.so BiLin.o RcppExports.o aSpline.o bilinear.o circum.o common.o convexHull.o init.o interp.o partDeriv.o s_hull_pro.o shullDeltri.o -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT5Of4m/R.INSTALL13ebd2719b480f/interp/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT5Of4m/R.INSTALL13ebd2719b480f/interp/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT5Of4m/R.INSTALL13ebd2719b480f/interp/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-interp/00new/interp/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 (interp)
  * installing *source* package ‘Biostrings’ ...
  ** this is package ‘Biostrings’ version ‘2.79.4’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHSJZBN/R.INSTALL16e7996df25379/Biostrings/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BAB_class.c -o BAB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
  BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
    299 | static void BitMatrix_print(BitMatrix *bitmat)
        |             ^~~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
  MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
    184 |         IntAE *poffsets, *poffsets_order;
        |                           ^~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
  SparseList_utils.c:42:27: error: use of undeclared identifier 'NAMED'
     42 |         if (ans != R_NilValue && NAMED(ans) == 0)
        |                                  ^~~~~
  SparseList_utils.c:43:3: error: use of undeclared identifier 'SET_NAMED'
     43 |                 SET_NAMED(ans, 1);
        |                 ^~~~~~~~~
  2 errors generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: SparseList_utils.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHSJZBN/R.INSTALL16e7996df25379/Biostrings/src'
  ERROR: compilation failed for package ‘Biostrings’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Biostrings’
  * installing *source* package ‘GenomicRanges’ ...
  ** this is package ‘GenomicRanges’ version ‘1.63.1’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpri7P7c/R.INSTALL16ebf421722944/GenomicRanges/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c transcript_utils.c -o transcript_utils.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpri7P7c/R.INSTALL16ebf421722944/GenomicRanges/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpri7P7c/R.INSTALL16ebf421722944/GenomicRanges/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpri7P7c/R.INSTALL16ebf421722944/GenomicRanges/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-GenomicRanges/00new/GenomicRanges/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 (GenomicRanges)
  * installing *source* package ‘SparseArray’ ...
  ** this is package ‘SparseArray’ version ‘1.11.10’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCt8lbb/R.INSTALL1739054ad161ff/SparseArray/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O3 -Wall -pedantic -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
  In file included from ExtendableJaggedArray.c:8:
  In file included from ./leaf_utils.h:6:
  ./SparseVec.h:125:16: error: use of undeclared identifier 'DATAPTR'
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
  1 error generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCt8lbb/R.INSTALL1739054ad161ff/SparseArray/src'
  ERROR: compilation failed for package ‘SparseArray’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/SparseArray’
  * installing *source* package ‘futile.logger’ ...
  ** this is package ‘futile.logger’ version ‘1.4.9’
  ** package ‘futile.logger’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (futile.logger)
  ERROR: dependency ‘Biostrings’ is not available for package ‘cigarillo’
  Perhaps try a variation of:
  install.packages('Biostrings')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/cigarillo’
  ERROR: dependency ‘Biostrings’ is not available for package ‘pwalign’
  Perhaps try a variation of:
  install.packages('Biostrings')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/pwalign’
  * installing *source* package ‘latticeExtra’ ...
  ** this is package ‘latticeExtra’ version ‘0.6-31’
  ** package ‘latticeExtra’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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
  * DONE (latticeExtra)
  ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’
  Perhaps try a variation of:
  install.packages('SparseArray')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/DelayedArray’
  Warning: SystemRequirements specified C++11: support has been removed
  * installing *source* package ‘BiocParallel’ ...
  ** this is package ‘BiocParallel’ version ‘1.45.0’
  ** using staged installation
  checking whether the C++ compiler works... yes
  checking for C++ compiler default output file name... a.out
  checking for suffix of executables... 
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether the compiler supports GNU C++... yes
  checking whether clang++-21 -std=gnu++20 accepts -g... yes
  checking for clang++-21 -std=gnu++20 option to enable C++11 features... none needed
  checking for library containing shm_open... none required
  checking for stdio.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for strings.h... yes
  checking for sys/stat.h... yes
  checking for sys/types.h... yes
  checking for unistd.h... yes
  checking for sys/mman.h... yes
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  specified C++11
  using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvJbswj/R.INSTALL1757034840ef5f/BiocParallel/src'
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I"./" -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/BH/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c cpp11.cpp -o cpp11.o
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I"./" -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/BH/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c ipcmutex.cpp -o ipcmutex.o
  clang++-21 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o BiocParallel.so cpp11.o ipcmutex.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvJbswj/R.INSTALL1757034840ef5f/BiocParallel/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvJbswj/R.INSTALL1757034840ef5f/BiocParallel/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvJbswj/R.INSTALL1757034840ef5f/BiocParallel/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel)
  ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
  Perhaps try a variation of:
  install.packages('DelayedArray')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/SummarizedExperiment’
  ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’
  Perhaps try a variation of:
  install.packages('Biostrings')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rsamtools’
  ERROR: dependencies ‘SummarizedExperiment’, ‘Biostrings’, ‘Rsamtools’, ‘cigarillo’ are not available for package ‘GenomicAlignments’
  Perhaps try a variation of:
  install.packages(c('SummarizedExperiment', 'Biostrings', 'Rsamtools', 'cigarillo'))
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/GenomicAlignments’
  ERROR: dependencies ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’, ‘pwalign’ are not available for package ‘ShortRead’
  Perhaps try a variation of:
  install.packages(c('Biostrings', 'Rsamtools', 'GenomicAlignments', 'pwalign'))
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/ShortRead’
  
  The downloaded source packages are in
  	'/home/hornik/tmp/scratch/Rtmp7vDA8M/downloaded_packages'
  Old packages: 'BiocGenerics', 'IRanges', 'Rsubread', 'S4Vectors', 'XVector',
    'edgeR', 'limma', 'systemfonts'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///srv/R/Repositories/CRAN
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-04 r89535)
  Installing package(s) 'rtracklayer'
  also installing the dependencies 'SparseArray', 'DelayedArray', 'SummarizedExperiment', 'cigarillo', 'RCurl', 'rjson', 'XML', 'Biostrings', 'Rsamtools', 'GenomicAlignments', 'BiocIO', 'restfulr'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/cigarillo_1.1.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicAlignments_1.47.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocIO_1.21.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/rtracklayer_1.71.3.tar.gz'
  * installing *source* package ‘SparseArray’ ...
  ** this is package ‘SparseArray’ version ‘1.11.10’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6DNthx/R.INSTALL17a15b3819586a/SparseArray/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O3 -Wall -pedantic -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
  In file included from ExtendableJaggedArray.c:8:
  In file included from ./leaf_utils.h:6:
  ./SparseVec.h:125:16: error: use of undeclared identifier 'DATAPTR'
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
  1 error generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6DNthx/R.INSTALL17a15b3819586a/SparseArray/src'
  ERROR: compilation failed for package ‘SparseArray’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/SparseArray’
  * installing *source* package ‘RCurl’ ...
  ** this is package ‘RCurl’ version ‘1.98-1.17’
  ** package ‘RCurl’ successfully unpacked and MD5 sums checked
  ** using staged installation
  checking for curl-config... /usr/bin/curl-config
  checking for gcc... clang-21 -std=gnu23
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables... 
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether the compiler supports GNU C... yes
  checking whether clang-21 -std=gnu23 accepts -g... yes
  checking for clang-21 -std=gnu23 option to enable C11 features... -std=gnu11
  checking how to run the C preprocessor... clang-21 -std=gnu23 -std=gnu11 -E
  Version has a libidn field
  Version has CURLOPT_URL
  Version has CURLINFO_EFFECTIVE_URL
  Version has CURLINFO_RESPONSE_CODE
  Version has CURLINFO_TOTAL_TIME
  Version has CURLINFO_NAMELOOKUP_TIME
  Version has CURLINFO_CONNECT_TIME
  Version has CURLINFO_PRETRANSFER_TIME
  Version has CURLINFO_SIZE_UPLOAD
  Version has CURLINFO_SIZE_DOWNLOAD
  Version has CURLINFO_SPEED_DOWNLOAD
  Version has CURLINFO_SPEED_UPLOAD
  Version has CURLINFO_HEADER_SIZE
  Version has CURLINFO_REQUEST_SIZE
  Version has CURLINFO_SSL_VERIFYRESULT
  Version has CURLINFO_FILETIME
  Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
  Version has CURLINFO_CONTENT_LENGTH_UPLOAD
  Version has CURLINFO_STARTTRANSFER_TIME
  Version has CURLINFO_CONTENT_TYPE
  Version has CURLINFO_REDIRECT_TIME
  Version has CURLINFO_REDIRECT_COUNT
  Version has CURLINFO_PRIVATE
  Version has CURLINFO_HTTP_CONNECTCODE
  Version has CURLINFO_HTTPAUTH_AVAIL
  Version has CURLINFO_PROXYAUTH_AVAIL
  Version has CURLINFO_OS_ERRNO
  Version has CURLINFO_NUM_CONNECTS
  Version has CURLINFO_SSL_ENGINES
  Version has CURLINFO_COOKIELIST
  Version has CURLINFO_LASTSOCKET
  Version has CURLINFO_FTP_ENTRY_PATH
  Version has CURLINFO_REDIRECT_URL
  Version has CURLINFO_PRIMARY_IP
  Version has CURLINFO_APPCONNECT_TIME
  Version has CURLINFO_CERTINFO
  Version has CURLINFO_CONDITION_UNMET
  Version has CURLOPT_WRITEDATA
  Version has CURLOPT_KEYPASSWD
  Version has CURLOPT_DIRLISTONLY
  Version has CURLOPT_APPEND
  Version has CURLOPT_KRBLEVEL
  Version has CURLOPT_USE_SSL
  Version has CURLOPT_TIMEOUT_MS
  Version has CURLOPT_CONNECTTIMEOUT_MS
  Version has CURLOPT_HTTP_TRANSFER_DECODING
  Version has CURLOPT_HTTP_CONTENT_DECODING
  Version has CURLOPT_NEW_FILE_PERMS
  Version has CURLOPT_NEW_DIRECTORY_PERMS
  Version has CURLOPT_POSTREDIR
  Version has CURLOPT_OPENSOCKETFUNCTION
  Version has CURLOPT_OPENSOCKETDATA
  Version has CURLOPT_COPYPOSTFIELDS
  Version has CURLOPT_PROXY_TRANSFER_MODE
  Version has CURLOPT_SEEKFUNCTION
  Version has CURLOPT_SEEKDATA
  Version has CURLOPT_CRLFILE
  Version has CURLOPT_ISSUERCERT
  Version has CURLOPT_ADDRESS_SCOPE
  Version has CURLOPT_CERTINFO
  Version has CURLOPT_USERNAME
  Version has CURLOPT_PASSWORD
  Version has CURLOPT_PROXYUSERNAME
  Version has CURLOPT_PROXYPASSWORD
  Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5
  Version has CURLOPT_NOPROXY
  Version has CURLOPT_TFTP_BLKSIZE
  Version has CURLOPT_SOCKS5_GSSAPI_SERVICE
  Version has CURLOPT_SOCKS5_GSSAPI_NEC
  Version has CURLOPT_PROTOCOLS
  Version has CURLOPT_REDIR_PROTOCOLS
  Version has CURLOPT_SSH_AUTH_TYPES
  Version has CURLOPT_SSH_PUBLIC_KEYFILE
  Version has CURLOPT_SSH_PRIVATE_KEYFILE
  Version has CURLOPT_FTP_SSL_CCC
  Version has CURLOPT_COOKIELIST
  Version has CURLOPT_IGNORE_CONTENT_LENGTH
  Version has CURLOPT_FTP_SKIP_PASV_IP
  Version has CURLOPT_FTP_FILEMETHOD
  Version has CURLOPT_LOCALPORT
  Version has CURLOPT_LOCALPORTRANGE
  Version has CURLOPT_CONNECT_ONLY
  Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION
  Version has CURLOPT_CONV_TO_NETWORK_FUNCTION
  Version has CURLOPT_CONV_FROM_UTF8_FUNCTION
  Version has CURLOPT_MAX_SEND_SPEED_LARGE
  Version has CURLOPT_MAX_RECV_SPEED_LARGE
  Version has CURLOPT_FTP_ALTERNATIVE_TO_USER
  Version has CURLOPT_SOCKOPTFUNCTION
  Version has CURLOPT_SOCKOPTDATA
  Version has CURLOPT_SSL_SESSIONID_CACHE
  libcurl version: libcurl 8.18.0
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpD3EU8v/R.INSTALL17a3805e696851/RCurl/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c base64.c -o base64.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c curl.c -o curl.o
  curl.c:212:14: warning: call to 'Wcurl_easy_setopt_err_long' declared with 'warning' attribute: curl_easy_setopt expects a long argument [-Wattribute-warning]
    212 |                         status =  curl_easy_setopt(obj, CURLOPT_POSTFIELDSIZE, Rf_length(el));
        |                                   ^
  /usr/include/x86_64-linux-gnu/curl/typecheck-gcc.h:50:15: note: expanded from macro 'curl_easy_setopt'
     50 |               Wcurl_easy_setopt_err_long();                             \
        |               ^
  curl.c:194:14: warning: call to 'Wcurl_easy_setopt_err_progress_cb' declared with 'warning' attribute: curl_easy_setopt expects a curl_progress_callback argument [-Wattribute-warning]
    194 |                         status =  curl_easy_setopt(obj, opt, &R_curl_progress_callback);
        |                                   ^
  /usr/include/x86_64-linux-gnu/curl/typecheck-gcc.h:81:15: note: expanded from macro 'curl_easy_setopt'
     81 |               Wcurl_easy_setopt_err_progress_cb();                      \
        |               ^
  curl.c:187:14: warning: call to 'Wcurl_easy_setopt_err_write_callback' declared with 'warning' attribute: curl_easy_setopt expects a curl_write_callback argument [-Wattribute-warning]
    187 |                         status =  curl_easy_setopt(obj, opt, &R_curl_write_header_data);
        |                                   ^
  /usr/include/x86_64-linux-gnu/curl/typecheck-gcc.h:60:15: note: expanded from macro 'curl_easy_setopt'
     60 |               Wcurl_easy_setopt_err_write_callback();                   \
        |               ^
  curl.c:179:14: warning: call to 'Wcurl_easy_setopt_err_debug_cb' declared with 'warning' attribute: curl_easy_setopt expects a curl_debug_callback argument [-Wattribute-warning]
    179 |                         status =  curl_easy_setopt(obj, opt, &R_curl_debug_callback);
        |                                   ^
  /usr/include/x86_64-linux-gnu/curl/typecheck-gcc.h:87:15: note: expanded from macro 'curl_easy_setopt'
     87 |               Wcurl_easy_setopt_err_debug_cb();                         \
        |               ^
  curl.c:169:14: warning: call to 'Wcurl_easy_setopt_err_write_callback' declared with 'warning' attribute: curl_easy_setopt expects a curl_write_callback argument [-Wattribute-warning]
    169 |                         status =  curl_easy_setopt(obj, CURLOPT_WRITEFUNCTION, &R_curl_write_data);
        |                                   ^
  /usr/include/x86_64-linux-gnu/curl/typecheck-gcc.h:60:15: note: expanded from macro 'curl_easy_setopt'
     60 |               Wcurl_easy_setopt_err_write_callback();                   \
        |               ^
  curl.c:171:14: warning: call to 'Wcurl_easy_setopt_err_write_callback' declared with 'warning' attribute: curl_easy_setopt expects a curl_write_callback argument [-Wattribute-warning]
    171 |                         status =  curl_easy_setopt(obj, CURLOPT_HEADERFUNCTION, &R_curl_write_header_data);
        |                                   ^
  /usr/include/x86_64-linux-gnu/curl/typecheck-gcc.h:60:15: note: expanded from macro 'curl_easy_setopt'
     60 |               Wcurl_easy_setopt_err_write_callback();                   \
        |               ^
  6 warnings generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c curlInit.c -o curlInit.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c curl_base64.c -o curl_base64.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c enums.c -o enums.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c json.c -o json.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c memoryManagement.c -o memoryManagement.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c myUTF8.c -o myUTF8.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpD3EU8v/R.INSTALL17a3805e696851/RCurl/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpD3EU8v/R.INSTALL17a3805e696851/RCurl/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpD3EU8v/R.INSTALL17a3805e696851/RCurl/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-RCurl/00new/RCurl/libs
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (RCurl)
  * installing *source* package ‘rjson’ ...
  ** this is package ‘rjson’ version ‘0.2.23’
  ** package ‘rjson’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9Opgbw/R.INSTALL17e2cf1e807a16/rjson/src'
  clang++-21 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c dump.cpp -o dump.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c parser.c -o parser.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c register.c -o register.o
  clang++-21 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o rjson.so dump.o parser.o register.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9Opgbw/R.INSTALL17e2cf1e807a16/rjson/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9Opgbw/R.INSTALL17e2cf1e807a16/rjson/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9Opgbw/R.INSTALL17e2cf1e807a16/rjson/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-rjson/00new/rjson/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 (rjson)
  * installing *source* package ‘XML’ ...
  ** this is package ‘XML’ version ‘3.99-0.22’
  ** package ‘XML’ successfully unpacked and MD5 sums checked
  ** using staged installation
  checking for gcc... clang-21 -std=gnu23
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables... 
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether the compiler supports GNU C... yes
  checking whether clang-21 -std=gnu23 accepts -g... yes
  checking for clang-21 -std=gnu23 option to enable C11 features... none needed
  checking how to run the C preprocessor... clang-21 -std=gnu23 -E
  checking for sed... /usr/bin/sed
  checking for pkg-config... /usr/bin/pkg-config
  checking for xml2-config... /usr/bin/xml2-config
  USE_XML2 = yes
  SED_EXTENDED_ARG: -E
  Minor 15, Patch 1 for 2.15.1
  Located parser file -I/usr/include/libxml2/parser.h
  Checking for 1.8:  -I/usr/include/libxml2
  Using libxml2.*
  checking for gzopen in -lz... yes
  checking for xmlParseFile in -lxml2... yes
  checking for xmlHashSize in -lxml2... yes
  Using built-in xmlHashSize
  Checking DTD parsing (presence of externalSubset)...
  checking for xmlHashSize in -lxml2... (cached) yes
  Found xmlHashSize
  checking for xmlOutputBufferCreateBuffer in -lxml2... yes
  have xmlOutputBufferCreateBuffer()
  checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes
  checking for libxml/xmlversion.h... yes
  Expat:  FALSE
  Checking for return type of xmlHashScan element routine.
  No return value for xmlHashScan
  xmlNs has a context field
  Checking for cetype_t enumeration
  Using recent version of R with cetype_t enumeration type for encoding
  checking for xmlsec1-config... no
  nodegc default 
  xml-debug default 
  Version has XML_WITH_ZLIB
  Version has xmlHasFeature()
  
  ****************************************
  Configuration information:
  
  Libxml settings
  
  libxml include directory: -I/usr/include/libxml2
  libxml library directory: -lxml2 -lz  -lxml2
  libxml 2:                 -DLIBXML2=1
  
  Compilation flags:         -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 
  Link flags:               -lxml2 -lz  -lxml2
  
  ****************************************
  configure: creating ./config.status
  config.status: creating src/Makevars
  config.status: creating R/supports.R
  config.status: creating inst/scripts/RSXML.csh
  config.status: creating inst/scripts/RSXML.bsh
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3QnkHf/R.INSTALL17ed8e580b68a2/XML/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c DocParse.c -o DocParse.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c EventParse.c -o EventParse.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c ExpatParse.c -o ExpatParse.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c HTMLParse.c -o HTMLParse.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c NodeGC.c -o NodeGC.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c RUtils.c -o RUtils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c Rcatalog.c -o Rcatalog.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c Utils.c -o Utils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c XMLEventParse.c -o XMLEventParse.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c XMLHashTree.c -o XMLHashTree.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c XMLTree.c -o XMLTree.o
  XMLTree.c:1415:9: warning: unused variable 'oldIndent' [-Wunused-variable]
   1415 |     int oldIndent;
        |         ^~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c fixNS.c -o fixNS.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c libxmlFeatures.c -o libxmlFeatures.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c schema.c -o schema.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c xmlsecurity.c -o xmlsecurity.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c xpath.c -o xpath.o
  xpath.c:255:15: warning: assigning to 'xmlXPathFunction' (aka 'void (*)(struct _xmlXPathParserContext *, int)') from 'void *' converts between void pointer and function pointer [-Wpedantic]
    255 |              routine = R_ExternalPtrAddr(el);
        |                      ^ ~~~~~~~~~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -lxml2 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3QnkHf/R.INSTALL17ed8e580b68a2/XML/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3QnkHf/R.INSTALL17ed8e580b68a2/XML/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3QnkHf/R.INSTALL17ed8e580b68a2/XML/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-XML/00new/XML/libs
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
  in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
  in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
  in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (XML)
  * installing *source* package ‘Biostrings’ ...
  ** this is package ‘Biostrings’ version ‘2.79.4’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptYfZBm/R.INSTALL1833384dd34d49/Biostrings/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BAB_class.c -o BAB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
  BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
    299 | static void BitMatrix_print(BitMatrix *bitmat)
        |             ^~~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
  MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
    184 |         IntAE *poffsets, *poffsets_order;
        |                           ^~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
  SparseList_utils.c:42:27: error: use of undeclared identifier 'NAMED'
     42 |         if (ans != R_NilValue && NAMED(ans) == 0)
        |                                  ^~~~~
  SparseList_utils.c:43:3: error: use of undeclared identifier 'SET_NAMED'
     43 |                 SET_NAMED(ans, 1);
        |                 ^~~~~~~~~
  2 errors generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: SparseList_utils.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptYfZBm/R.INSTALL1833384dd34d49/Biostrings/src'
  ERROR: compilation failed for package ‘Biostrings’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Biostrings’
  * installing *source* package ‘BiocIO’ ...
  ** this is package ‘BiocIO’ version ‘1.21.0’
  ** using staged installation
  ** 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
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  * DONE (BiocIO)
  ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’
  Perhaps try a variation of:
  install.packages('SparseArray')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/DelayedArray’
  ERROR: dependency ‘Biostrings’ is not available for package ‘cigarillo’
  Perhaps try a variation of:
  install.packages('Biostrings')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/cigarillo’
  ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’
  Perhaps try a variation of:
  install.packages('Biostrings')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rsamtools’
  * installing *source* package ‘restfulr’ ...
  ** this is package ‘restfulr’ version ‘0.0.16’
  ** package ‘restfulr’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8bHdPH/R.INSTALL1843c62f9d702f/restfulr/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c raggedListToDF.c -o raggedListToDF.o
  clang-21 -std=gnu23 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o restfulr.so init.o raggedListToDF.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8bHdPH/R.INSTALL1843c62f9d702f/restfulr/src'
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8bHdPH/R.INSTALL1843c62f9d702f/restfulr/src'
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8bHdPH/R.INSTALL1843c62f9d702f/restfulr/src'
  installing to /home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/00LOCK-restfulr/00new/restfulr/libs
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Creating a new generic function for ‘assign’ in package ‘restfulr’
  ** help
  *** installing help indices
  ** building package indices
  ** 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 (restfulr)
  ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
  Perhaps try a variation of:
  install.packages('DelayedArray')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/SummarizedExperiment’
  ERROR: dependencies ‘SummarizedExperiment’, ‘Biostrings’, ‘Rsamtools’, ‘cigarillo’ are not available for package ‘GenomicAlignments’
  Perhaps try a variation of:
  install.packages(c('SummarizedExperiment', 'Biostrings', 'Rsamtools', 'cigarillo'))
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/GenomicAlignments’
  ERROR: dependencies ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
  Perhaps try a variation of:
  install.packages(c('Biostrings', 'Rsamtools', 'GenomicAlignments'))
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/rtracklayer’
  
  The downloaded source packages are in
  	'/home/hornik/tmp/scratch/Rtmp7vDA8M/downloaded_packages'
  Old packages: 'BiocGenerics', 'IRanges', 'Rsubread', 'S4Vectors', 'XVector',
    'edgeR', 'limma', 'systemfonts'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///srv/R/Repositories/CRAN
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-04 r89535)
  Installing package(s) 'Rsamtools'
  also installing the dependency 'Biostrings'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz'
  * installing *source* package ‘Biostrings’ ...
  ** this is package ‘Biostrings’ version ‘2.79.4’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXGNYDq/R.INSTALL18651a6bcf1886/Biostrings/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BAB_class.c -o BAB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
  BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
    299 | static void BitMatrix_print(BitMatrix *bitmat)
        |             ^~~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
  MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
    184 |         IntAE *poffsets, *poffsets_order;
        |                           ^~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
  SparseList_utils.c:42:27: error: use of undeclared identifier 'NAMED'
     42 |         if (ans != R_NilValue && NAMED(ans) == 0)
        |                                  ^~~~~
  SparseList_utils.c:43:3: error: use of undeclared identifier 'SET_NAMED'
     43 |                 SET_NAMED(ans, 1);
        |                 ^~~~~~~~~
  2 errors generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: SparseList_utils.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXGNYDq/R.INSTALL18651a6bcf1886/Biostrings/src'
  ERROR: compilation failed for package ‘Biostrings’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Biostrings’
  ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’
  Perhaps try a variation of:
  install.packages('Biostrings')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Rsamtools’
  
  The downloaded source packages are in
  	'/home/hornik/tmp/scratch/Rtmp7vDA8M/downloaded_packages'
  Old packages: 'BiocGenerics', 'IRanges', 'Rsubread', 'S4Vectors', 'XVector',
    'edgeR', 'limma', 'systemfonts'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///srv/R/Repositories/CRAN
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-04 r89535)
  Installing package(s) 'HTSFilter'
  also installing the dependencies 'SparseArray', 'DelayedArray', 'SummarizedExperiment', 'DESeq2'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DESeq2_1.51.6.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/HTSFilter_1.51.0.tar.gz'
  * installing *source* package ‘SparseArray’ ...
  ** this is package ‘SparseArray’ version ‘1.11.10’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpr1BAVr/R.INSTALL18735a63089162/SparseArray/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -fpic  -g -O3 -Wall -pedantic -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
  In file included from ExtendableJaggedArray.c:8:
  In file included from ./leaf_utils.h:6:
  ./SparseVec.h:125:16: error: use of undeclared identifier 'DATAPTR'
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
  1 error generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpr1BAVr/R.INSTALL18735a63089162/SparseArray/src'
  ERROR: compilation failed for package ‘SparseArray’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/SparseArray’
  ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’
  Perhaps try a variation of:
  install.packages('SparseArray')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/DelayedArray’
  ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
  Perhaps try a variation of:
  install.packages('DelayedArray')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/SummarizedExperiment’
  ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘DESeq2’
  Perhaps try a variation of:
  install.packages('SummarizedExperiment')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/DESeq2’
  ERROR: dependency ‘DESeq2’ is not available for package ‘HTSFilter’
  Perhaps try a variation of:
  install.packages('DESeq2')
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/HTSFilter’
  
  The downloaded source packages are in
  	'/home/hornik/tmp/scratch/Rtmp7vDA8M/downloaded_packages'
  Old packages: 'BiocGenerics', 'IRanges', 'Rsubread', 'S4Vectors', 'XVector',
    'edgeR', 'limma', 'systemfonts'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///srv/R/Repositories/CRAN
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-04 r89535)
  Installing package(s) 'Biostrings'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz'
  Content type 'application/x-gzip' length 12813727 bytes (12.2 MB)
  ==================================================
  downloaded 12.2 MB
  
  * installing *source* package ‘Biostrings’ ...
  ** this is package ‘Biostrings’ version ‘2.79.4’
  ** using staged installation
  ** libs
  using C compiler: ‘Debian clang version 21.1.8 (3+b1)’
  make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOSJT9W/R.INSTALL187e3176152dbb/Biostrings/src'
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BAB_class.c -o BAB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c BitMatrix.c -o BitMatrix.o
  BitMatrix.c:299:13: warning: unused function 'BitMatrix_print' [-Wunused-function]
    299 | static void BitMatrix_print(BitMatrix *bitmat)
        |             ^~~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c MIndex_class.c -o MIndex_class.o
  MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
    184 |         IntAE *poffsets, *poffsets_order;
        |                           ^~~~~~~~~~~~~~
  1 warning generated.
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c R_init_Biostrings.c -o R_init_Biostrings.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c RoSeqs_utils.c -o RoSeqs_utils.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/S4Vectors/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/IRanges/include' -I'/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/XVector/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c SparseList_utils.c -o SparseList_utils.o
  SparseList_utils.c:42:27: error: use of undeclared identifier 'NAMED'
     42 |         if (ans != R_NilValue && NAMED(ans) == 0)
        |                                  ^~~~~
  SparseList_utils.c:43:3: error: use of undeclared identifier 'SET_NAMED'
     43 |                 SET_NAMED(ans, 1);
        |                 ^~~~~~~~~
  2 errors generated.
  make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: SparseList_utils.o] Error 1
  make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOSJT9W/R.INSTALL187e3176152dbb/Biostrings/src'
  ERROR: compilation failed for package ‘Biostrings’
  * removing ‘/home/hornik/tmp/scratch/RtmpHL97Om/RLIBS_10c7564b9a9e3c/Biostrings’
  
  The downloaded source packages are in
  	'/home/hornik/tmp/scratch/Rtmp7vDA8M/downloaded_packages'
  Old packages: 'BiocGenerics', 'IRanges', 'Rsubread', 'S4Vectors', 'XVector',
    'edgeR', 'limma', 'systemfonts'
  Saving _problems/test-inDAGO_shiny-26.R
  [ FAIL 1 | WARN 25 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-inDAGO_shiny.R:26:3'): Shiny app is generated ──────────────────
  Error in `inDAGO()`: The following packages are not installed: ShortRead, rtracklayer, Rsamtools, HTSFilter, Biostrings.
  To enable all the features of inDAGO install with:
    if (!requireNamespace('BiocManager', quietly=TRUE))
      install.packages('BiocManager')
    BiocManager::install(c("ShortRead", "rtracklayer", "Rsamtools", "HTSFilter", "Biostrings"))
  
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(inDAGO(), "shiny.appobj") at test-inDAGO_shiny.R:26:3
   2. │ └─testthat::quasi_label(enquo(object))
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─inDAGO::inDAGO()
  
  [ FAIL 1 | WARN 25 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

OK r-devel-linux-x86_64-debian-gcc

OK r-devel-linux-x86_64-fedora-clang

NOTE r-devel-linux-x86_64-fedora-gcc

for non-standard things in the check directory

Found the following files/directories:
  ‘HTSFilter’

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

OK r-oldrel-macos-arm64

NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘Rsubread’

OK r-oldrel-windows-x86_64

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Additional Issues

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ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-devel-linux-x86_64-debian-clang

tests

  Running ‘testthat.R’ [11m/15m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > # library("testthat")
  > # li

NOTE r-devel-linux-x86_64-fedora-gcc

for non-standard things in the check directory

Found the following files/directories:
  ‘HTSFilter’

NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘Rsubread’

Dependency Network

Version History

new 1.0.3 Mar 9, 2026