* installing *source* package ‘vcfppR’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 17.0.5 (1)’ clang++-17 -std=gnu++17 -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 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ In file included from RcppExports.cpp:4: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~~~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. clang++-17 -std=gnu++17 -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 -c vcf-reader.cpp -o vcf-reader.o In file included from vcf-reader.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ In file included from vcf-reader.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~~~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. clang++-17 -std=gnu++17 -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 -c vcf-writer.cpp -o vcf-writer.o In file included from vcf-writer.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ In file included from vcf-writer.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~~~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. clang++-17 -std=gnu++17 -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 -c vcfpp-popgen.cpp -o vcfpp-popgen.o In file included from vcfpp-popgen.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ In file included from vcfpp-popgen.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~~~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. clang++-17 -std=gnu++17 -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 -c vcfpp-read.cpp -o vcfpp-read.o In file included from vcfpp-read.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ In file included from vcfpp-read.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~~~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. clang++-17 -std=gnu++17 -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 -c vcfpp-stats.cpp -o vcfpp-stats.o In file included from vcfpp-stats.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:128: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/routines.h:26: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ In file included from vcfpp-stats.cpp:1: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27: In file included from /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:181: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 30 | Rf_warningcall(call, s.c_str()); | ^~~~~~~~~ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include/Rcpp/print.h:30:26: note: treat the string as an argument to avoid this 30 | Rf_warningcall(call, s.c_str()); | ^ | "%s", 3 warnings generated. (cd htslib-1.18 && make -f Makefile.vcfppR libhts.a && cd ..) make[1]: Entering directory '/srv/hornik/tmp/CRAN/vcfppR.Rcheck/00_pkg_src/vcfppR/src/htslib-1.18' echo '/* Default config.h generated by Makefile */' > config.h echo '#ifndef _XOPEN_SOURCE' >> config.h echo '#define _XOPEN_SOURCE 600' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_DRAND48 1' >> config.h echo '#define HAVE_LIBCURL 1' >> config.h if [ "x" != "x" ] && \ [ "x" != "x" ] && \ [ "x" != "x" ]; then \ echo '#define HAVE_POPCNT 1' >> config.h ; \ echo '#define HAVE_SSE4_1 1' >> config.h ; \ echo '#define HAVE_SSSE3 1' >> config.h ; \ echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \ echo '#define UBSAN 1' >> config.h ; \ echo '#endif' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX2 1' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX512 1' >> config.h ; \ fi clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o kfunc.o kfunc.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o kstring.o kstring.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o bgzf.o bgzf.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o errmod.o errmod.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o faidx.o faidx.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 2298 | sam_hrecs_t *sam_hrecs_new() { | ^ | void 1 warning generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 958 | 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] 1060 | 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-17' \ '' \ '-g -O3 -Wall -pedantic -fpic -fvisibility=hidden' \ '-Wl,-O1 -fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 53 | 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] 84 | 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] 4903 | 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] 4917 | enum htsLogLevel hts_get_log_level() | ^ | void 4 warnings generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o hts_os.o hts_os.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o md5.o md5.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o multipart.o multipart.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o probaln.o probaln.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o realn.o realn.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o regidx.o regidx.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o region.o region.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 103 | 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] 413 | bam1_t *bam_init1() | ^ | void 2 warnings generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o tbx.o tbx.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 223 | hts_json_token * hts_json_alloc_token() { | ^ | void 1 warning generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 1522 | bcf1_t *bcf_init() | ^ | void 1 warning generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c htscodecs/htscodecs/fqzcomp_qual.c:274:13: warning: unused function 'dump_params' [-Wunused-function] 274 | static void dump_params(fqz_gparams *gp) { | ^~~~~~~~~~~ 1 warning generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 53 | 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] 42 | const char *htscodecs_version() { | ^ | void 2 warnings generated. clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang-17 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -I. -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] 280 | static void libcurl_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 ranlib libhts.a make[1]: Leaving directory '/srv/hornik/tmp/CRAN/vcfppR.Rcheck/00_pkg_src/vcfppR/src/htslib-1.18' clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o vcfppR.so RcppExports.o vcf-reader.o vcf-writer.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)