Last updated on 2026-03-08 00:49:23 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 25.17 | 882.42 | 907.59 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 18.83 | 230.30 | 249.13 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 49.00 | 729.35 | 778.35 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 44.00 | 962.73 | 1006.73 | NOTE | |
| r-devel-macos-arm64 | 1.0.3 | 16.00 | 85.00 | 101.00 | OK | |
| r-devel-windows-x86_64 | 1.0.3 | 63.00 | 301.00 | 364.00 | OK | |
| r-patched-linux-x86_64 | 1.0.3 | 26.57 | 311.64 | 338.21 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 25.87 | 309.75 | 335.62 | OK | |
| r-release-macos-arm64 | 1.0.3 | OK | ||||
| r-release-macos-x86_64 | 1.0.3 | 38.00 | 454.00 | 492.00 | OK | |
| r-release-windows-x86_64 | 1.0.3 | 58.00 | 303.00 | 361.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.3 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.3 | 39.00 | 572.00 | 611.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.0.3 | 86.00 | 389.00 | 475.00 | OK |
Version: 1.0.3
Check: tests
Result: ERROR
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.3
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘HTSFilter’
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘Rsubread’
Flavor: r-oldrel-macos-x86_64