* installing *source* package ‘vcfppR’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 16.0.6 (15)’ using C++11 clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c RcppExports.cpp -o RcppExports.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-filter.cpp -o vcfpp-filter.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-popgen.cpp -o vcfpp-popgen.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-read.cpp -o vcfpp-read.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-stats.cpp -o vcfpp-stats.o (cd htslib-1.18 && ./configure && make libhts.a CC="clang-16 " AR="ar" RANLIB="ranlib" CFLAGS="-g -O3 -Wall -pedantic" CPPFLAGS="-I/usr/local/include -fPIC" LDFLAGS="-Wl,-O1" && cd ..) checking for gcc... gcc 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no 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 for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes 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 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 libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... 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 make[1]: Entering directory '/srv/hornik/tmp/CRAN/vcfppR.Rcheck/00_pkg_src/vcfppR/src/htslib-1.18' clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o kfunc.o kfunc.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o kstring.o kstring.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o bcf_sr_sort.o bcf_sr_sort.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o bgzf.o bgzf.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o errmod.o errmod.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o faidx.o faidx.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o header.o header.c header.c:2298:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] sam_hrecs_t *sam_hrecs_new() { ^ void 1 warning generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hfile.o hfile.c hfile.c:958:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] static void hfile_exit() ^ void hfile.c:1060:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] static int load_hfile_plugins() ^ void 2 warnings generated. 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-16 ' \ '-I/usr/local/include -fPIC' \ '-g -O3 -Wall -pedantic' \ '-Wl,-O1' \ '-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto' > config_vars.h clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hts.o hts.c In file included from hts.c:72: ./htscodecs/htscodecs/htscodecs.h:53:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] const char *htscodecs_version(); ^ void hts.c:84:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] const char *hts_version() ^ void hts.c:4903:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] void hts_lib_shutdown() ^ void hts.c:4917:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level() ^ void 4 warnings generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hts_expr.o hts_expr.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hts_os.o hts_os.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o md5.o md5.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o multipart.o multipart.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o probaln.o probaln.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o realn.o realn.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o regidx.o regidx.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o region.o region.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o sam.o sam.c sam.c:103:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] sam_hdr_t *sam_hdr_init() ^ void sam.c:413:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] bam1_t *bam_init1() ^ void 2 warnings generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o sam_mods.o sam_mods.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o synced_bcf_reader.o synced_bcf_reader.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o vcf_sweep.o vcf_sweep.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o tbx.o tbx.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o textutils.o textutils.c textutils.c:223:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token() { ^ void 1 warning generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o thread_pool.o thread_pool.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o vcf.o vcf.c vcf.c:1522:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] bcf1_t *bcf_init() ^ void 1 warning generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o vcfutils.o vcfutils.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_codecs.o cram/cram_codecs.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_decode.o cram/cram_decode.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_encode.o cram/cram_encode.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_external.o cram/cram_external.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_index.o cram/cram_index.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_io.o cram/cram_io.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/cram_stats.o cram/cram_stats.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/mFILE.o cram/mFILE.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/open_trace_file.o cram/open_trace_file.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o cram/string_alloc.o cram/string_alloc.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c In file included from htscodecs/htscodecs/htscodecs.c:34: htscodecs/htscodecs/htscodecs.h:53:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] const char *htscodecs_version(); ^ void htscodecs/htscodecs/htscodecs.c:42:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] const char *htscodecs_version() { ^ void 2 warnings generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang-16 -g -O3 -Wall -pedantic -mavx2 -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang-16 -g -O3 -Wall -pedantic -mavx512f -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang-16 -g -O3 -Wall -pedantic -msse4.1 -mpopcnt -mssse3 -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hfile_libcurl.o hfile_libcurl.c hfile_libcurl.c:280:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] static void libcurl_exit() ^ void 1 warning generated. clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hfile_gcs.o hfile_gcs.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hfile_s3.o hfile_s3.c clang-16 -g -O3 -Wall -pedantic -I. -I/usr/local/include -fPIC -c -o hfile_s3_write.o hfile_s3_write.c hfile_s3_write.c:825:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] static void s3_write_exit() { ^ void 1 warning generated. 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 hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a make[1]: Leaving directory '/srv/hornik/tmp/CRAN/vcfppR.Rcheck/00_pkg_src/vcfppR/src/htslib-1.18' clang++-16 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o vcfppR.so RcppExports.o vcfpp-filter.o vcfpp-popgen.o vcfpp-read.o vcfpp-stats.o htslib-1.18/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/vcfppR.Rcheck/00LOCK-vcfppR/00new/vcfppR/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 (vcfppR)