* installing *source* package ‘vcfppR’ ...
** using staged installation
Configuring HTSlib in src/htslib-1.21
checking for gcc... clang-19
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-19 accepts -g... yes
checking for clang-19 option to enable C11 features... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for clang-19 options needed to detect all undeclared functions... none needed
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/param.h... yes
checking whether _XOPEN_SOURCE is declared... no
checking whether __get_cpuid_max is declared... yes
checking whether __cpuid_count is declared... yes
checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt
checking C compiler flags needed for avx2... -mavx2 -mpopcnt
checking C compiler flags needed for avx512f... -mavx512f -mpopcnt
checking for working __builtin_cpu_supports("ssse3")... yes
checking for __attribute__((target))... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for clang-19 option to enable large file support... none needed
checking shared library type for unknown-Linux... plain .so
checking whether the linker supports versioned symbols... yes
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for __attribute__((constructor))... yes
checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... yes
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: linking htscodecs_bundled.mk to htscodecs.mk
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o kfunc.o kfunc.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o kstring.o kstring.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o bcf_sr_sort.o bcf_sr_sort.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o bgzf.o bgzf.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o errmod.o errmod.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o faidx.o faidx.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o header.o header.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.21"' > 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-19' \
'-I/usr/local/include' \
'-Wall -O2 -fPIC -fvisibility=hidden' \
'-Wl,-O1 -fvisibility=hidden ' \
'-llzma -lbz2 -lz -lm  -lcurl -lcrypto' > config_vars.h
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hts.o hts.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hts_expr.o hts_expr.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hts_os.o hts_os.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o md5.o md5.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o multipart.o multipart.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o probaln.o probaln.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o realn.o realn.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o regidx.o regidx.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o region.o region.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o sam.o sam.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o sam_mods.o sam_mods.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o simd.o simd.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o vcf_sweep.o vcf_sweep.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o tbx.o tbx.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o textutils.o textutils.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o thread_pool.o thread_pool.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o vcf.o vcf.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o vcfutils.o vcfutils.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_external.o cram/cram_external.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_index.o cram/cram_index.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/mFILE.o cram/mFILE.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
htscodecs/htscodecs/fqzcomp_qual.c:229:13: warning: unused function 'dump_table' [-Wunused-function]
  229 | static void dump_table(unsigned int *tab, int size, char *name) {
      |             ^~~~~~~~~~
htscodecs/htscodecs/fqzcomp_qual.c:264:13: warning: unused function 'dump_map' [-Wunused-function]
  264 | static void dump_map(unsigned int *map, int size, char *name) {
      |             ^~~~~~~~
2 warnings generated.
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden -mavx2 -mpopcnt -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden -mavx512f -mpopcnt -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hfile_gcs.o hfile_gcs.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hfile_s3.o hfile_s3.c
clang-19 -Wall -O2 -fPIC -fvisibility=hidden  -I. -I/usr/local/include -c -o hfile_s3_write.o hfile_s3_write.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 simd.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 hfile_gcs.o hfile_s3.o hfile_s3_write.o
ranlib libhts.a
** libs
using C++ compiler: ‘Debian clang version 19.1.5 (1)’
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf-popgen.cpp -o vcf-popgen.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf-reader.cpp -o vcf-reader.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf-stats.cpp -o vcf-stats.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf-table.cpp -o vcf-table.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf-writer.cpp -o vcf-writer.o
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o vcfppR.so RcppExports.o vcf-popgen.o vcf-reader.o vcf-stats.o vcf-table.o vcf-writer.o htslib-1.21/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl -L/home/hornik/tmp/R/lib -lR
installing to /srv/hornik/tmp/CRAN_pretest/vcfppR.Rcheck/00LOCK-vcfppR/00new/vcfppR/libs
** R
** 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 (vcfppR)