* installing *source* package 'vcfppR' ...
** package 'vcfppR' successfully unpacked and MD5 sums checked
** using staged installation
Configuring HTSlib in src/htslib-1.21
configure: loading site script /usr/local/etc/config.site
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc 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 gcc 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... /x86_64-w64-mingw32.static.posix/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for gcc option to enable large file support... -D_FILE_OFFSET_BITS=64
checking shared library type for unknown-MSYS_NT-10.0-20348... MSYS dll
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-pc-msys
checking host system type... x86_64-pc-msys
checking for getpagesize... yes
checking for working mmap... no
checking for gmtime_r... no
checking for fsync... no
checking for drand48... no
checking for srand48_deterministic... no
checking whether fdatasync is declared... no
checking for __attribute__((constructor))... yes
checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes
checking for library containing log... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... -lws2_32
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... no
checking for curl_easy_init in -lcurl... no
configure: WARNING: libcurl not enabled: library not found
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking for library containing regcomp... -lregex
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
make[1]: Entering directory '/d/temp/2024_12_25_01_50_00_20757/RtmpQB6Xmh/R.INSTALL2d3742e5c1256/vcfppR/src/htslib-1.21'
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o kfunc.o kfunc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o kstring.o kstring.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o bgzf.o bgzf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o errmod.o errmod.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o faidx.o faidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o header.o header.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -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' \
'gcc' \
'' \
'-Wall -O2 -fPIC -fvisibility=hidden' \
'-fvisibility=hidden ' \
'-lregex -llzma -lbz2 -lws2_32 -lz ' > config_vars.h
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hts.o hts.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o hts_os.o hts_os.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o md5.o md5.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o multipart.o multipart.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o probaln.o probaln.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o realn.o realn.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o regidx.o regidx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o region.o region.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o sam.o sam.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o simd.o simd.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o tbx.o tbx.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o textutils.o textutils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o vcf.o vcf.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -mavx2 -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -mavx512f -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -O2 -fPIC -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.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
ranlib libhts.a
make[1]: Leaving directory '/d/temp/2024_12_25_01_50_00_20757/RtmpQB6Xmh/R.INSTALL2d3742e5c1256/vcfppR/src/htslib-1.21'
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture
using C++ compiler: 'g++.exe (GCC) 12.3.0'
make[1]: Entering directory '/d/temp/2024_12_25_01_50_00_20757/RtmpQB6Xmh/R.INSTALL2d3742e5c1256/vcfppR/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools43/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.3/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
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools43/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-popgen.cpp -o vcf-popgen.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools43/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.3/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
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools43/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-stats.cpp -o vcf-stats.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools43/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-table.cpp -o vcf-table.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'htslib-1.21' -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools43/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.3/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
g++ -std=gnu++17 -shared -s -static-libgcc -o vcfppR.dll tmp.def RcppExports.o vcf-popgen.o vcf-reader.o vcf-stats.o vcf-table.o vcf-writer.o htslib-1.21/libhts.a -llzma -lbz2 -lregex -LD:/rtools43/x86_64-w64-mingw32.static.posix/lib -lcurl -lidn2 -lunistring -liconv -lcharset -lssh2 -lgcrypt -lgpg-error -lbcrypt -ladvapi32 -lssl -lcrypto -lcrypt32 -lgdi32 -lwldap32 -lzstd -lz -lws2_32 -lpthread -lidn2 -lunistring -liconv -lcharset -lssh2 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lgcrypt -lgpg-error -lws2_32 -lgcrypt -lgpg-error -lws2_32 -lz -lbcrypt -ladvapi32 -lcrypt32 -lssl -lcrypto -lssl -lz -lws2_32 -lgdi32 -lcrypt32 -lcrypto -lz -lws2_32 -lgdi32 -lcrypt32 -lgdi32 -lwldap32 -lzstd -lz -lws2_32 -lpthread -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_25_01_50_00_20757/RtmpQB6Xmh/R.INSTALL2d3742e5c1256/vcfppR/src'
make[1]: Entering directory '/d/temp/2024_12_25_01_50_00_20757/RtmpQB6Xmh/R.INSTALL2d3742e5c1256/vcfppR/src'
make[1]: Leaving directory '/d/temp/2024_12_25_01_50_00_20757/RtmpQB6Xmh/R.INSTALL2d3742e5c1256/vcfppR/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-vcfppR/00new/vcfppR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'vcfppR' as vcfppR_0.7.0.zip
* DONE (vcfppR)