* installing *source* package 'vcfppR' ... ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 12.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -Ihtslib-1.18 -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/routines.h:26, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:128, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27, from RcppExports.cpp:4: D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -Ihtslib-1.18 -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-reader.cpp -o vcf-reader.o In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/routines.h:26, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:128, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27, from vcf-reader.cpp:1: D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} vcf-reader.cpp: In member function 'double vcfreader::infoFloat(std::string)': vcf-reader.cpp:114:24: warning: 'f' may be used uninitialized [-Wmaybe-uninitialized] 114 | return (double)f; | ^ vcf-reader.cpp:112:15: note: 'f' was declared here 112 | float f; | ^ vcf-reader.cpp: In member function 'int vcfreader::infoInt(std::string)': vcf-reader.cpp:109:16: warning: 'i' may be used uninitialized [-Wmaybe-uninitialized] 109 | return i; | ^ vcf-reader.cpp:107:13: note: 'i' was declared here 107 | int i; | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -Ihtslib-1.18 -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-writer.cpp -o vcf-writer.o In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/routines.h:26, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:128, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27, from vcf-writer.cpp:1: D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -Ihtslib-1.18 -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcfpp-popgen.cpp -o vcfpp-popgen.o In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/routines.h:26, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:128, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27, from vcfpp-popgen.cpp:1: D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -Ihtslib-1.18 -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcfpp-read.cpp -o vcfpp-read.o In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/routines.h:26, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:128, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27, from vcfpp-read.cpp:1: D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I. -Ihtslib-1.18 -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcfpp-stats.cpp -o vcfpp-stats.o In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/routines.h:26, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:128, from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27, from vcfpp-stats.cpp:1: D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long long int]': D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long long int} cd htslib-1.18 && /usr/bin/make -f Makefile.win libhts.a && cd .. make[1]: Entering directory '/d/temp/Rtmpes3Egs/R.INSTALLf2acb3545bd/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_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 gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile.o hfile.c hfile.c:958:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 958 | static void hfile_exit() | ^~~~~~~~~~ hfile.c:1060:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] 1060 | static int load_hfile_plugins() | ^~~~~~~~~~~~~~~~~~ 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' \ 'gcc' \ '-D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB' \ '-pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden' \ '-fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex' > config_vars.h gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c In file included from hts.c:72: htscodecs/htscodecs/htscodecs.h:53:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] 53 | const char *htscodecs_version(); | ^~~~~ gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_expr.o hts_expr.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_os.o hts_os.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam_mods.o sam_mods.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c htscodecs/htscodecs/fqzcomp_qual.c:274:13: warning: 'dump_params' defined but not used [-Wunused-function] 274 | static void dump_params(fqz_gparams *gp) { | ^~~~~~~~~~~ gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c In file included from htscodecs/htscodecs/htscodecs.c:34: htscodecs/htscodecs/htscodecs.h:53:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] 53 | const char *htscodecs_version(); | ^~~~~ htscodecs/htscodecs/htscodecs.c:42:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 42 | const char *htscodecs_version() { | ^~~~~~~~~~~~~~~~~ gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile_libcurl.o hfile_libcurl.c hfile_libcurl.c:280:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 280 | static void libcurl_exit() | ^~~~~~~~~~~~ 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 '/d/temp/Rtmpes3Egs/R.INSTALLf2acb3545bd/vcfppR/src/htslib-1.18' D:\rtools43\x86_64-w64-mingw32.static.posix\bin\nm.exe: 'HTSLIB': No such file g++ -std=gnu++17 -shared -s -static-libgcc -o vcfppR.dll tmp.def RcppExports.o vcf-reader.o vcf-writer.o vcfpp-popgen.o vcfpp-read.o vcfpp-stats.o htslib-1.18/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-vcfppR/00new/vcfppR/libs/x64 ** 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 (vcfppR)