* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘jackalope’ ...
** this is package ‘jackalope’ version ‘1.1.5’
** package ‘jackalope’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 19.1.7 (3+b2)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1eMhAp/R.INSTALL22fa59709238fa/jackalope/src'
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./jackalope_types.h:15:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c alter_reference.cpp -o alter_reference.o
In file included from alter_reference.cpp:8:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c create_sequences.cpp -o create_sequences.o
In file included from create_sequences.cpp:13:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c hap_classes.cpp -o hap_classes.o
In file included from hap_classes.cpp:13:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c haps_ssites.cpp -o haps_ssites.o
In file included from haps_ssites.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c hts_illumina.cpp -o hts_illumina.o
In file included from hts_illumina.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c hts_pacbio.cpp -o hts_pacbio.o
In file included from hts_pacbio.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c io_fasta.cpp -o io_fasta.o
In file included from io_fasta.cpp:8:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c io_ms.cpp -o io_ms.o
In file included from io_ms.cpp:7:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c io_vcf.cpp -o io_vcf.o
In file included from io_vcf.cpp:7:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c mutator.cpp -o mutator.o
In file included from mutator.cpp:9:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c mutator_indels.cpp -o mutator_indels.o
In file included from mutator_indels.cpp:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c mutator_subs.cpp -o mutator_subs.o
In file included from mutator_subs.cpp:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c phylogenomics.cpp -o phylogenomics.o
In file included from phylogenomics.cpp:13:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c ref_hap_access.cpp -o ref_hap_access.o
In file included from ref_hap_access.cpp:14:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c sub_models.cpp -o sub_models.o
In file included from sub_models.cpp:16:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c util.cpp -o util.o
In file included from util.cpp:3:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o jackalope.so RcppExports.o alter_reference.o create_sequences.o hap_classes.o haps_ssites.o hts_illumina.o hts_pacbio.o io_fasta.o io_ms.o io_vcf.o mutator.o mutator_indels.o mutator_subs.o phylogenomics.o ref_hap_access.o sub_models.o util.o -lz -llzma -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1eMhAp/R.INSTALL22fa59709238fa/jackalope/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1eMhAp/R.INSTALL22fa59709238fa/jackalope/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1eMhAp/R.INSTALL22fa59709238fa/jackalope/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-jackalope/00new/jackalope/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (jackalope)