xinguo1236
commented
5 months ago - installing source package 'Rhtslib' ... using non-staged installation via StagedInstall field libs using C compiler: 'gcc.exe (GCC) 12.3.0' cd "htslib-1.18" && /usr/bin/make -f "Makefile.Rhtslib.win" make[1]: Entering directory '/c/Users/GuoX/AppData/Local/Temp/RtmpEjLmGs/R.INSTALLa7003e625e3d/Rhtslib/src/htslib-1.18' make[1]: D:/Program: No such file or directory make[1]: D:/Program: No such file or directory make[1]: D:/Program: No such file or directory make[1]: D:/Program: No such file or directory make[1]: D:/Program: No such file or directory make[1]: D:/Program: No such file or directory fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: kfunc.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: kstring.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: bcf_sr_sort.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: bgzf.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: errmod.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: faidx.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: header.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile.o hfile.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: hfile.o] Error 127 (ignored) 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' \ '' \ '-D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB' \ '-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 fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: hts.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_expr.o hts_expr.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: hts_expr.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_os.o hts_os.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: hts_os.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: md5.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: multipart.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: probaln.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: realn.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: regidx.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: region.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: sam.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam_mods.o sam_mods.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: sam_mods.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: synced_bcf_reader.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: vcf_sweep.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: tbx.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: textutils.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: thread_pool.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: vcf.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: vcfutils.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_codecs.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_decode.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_encode.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_external.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_index.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_io.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/cram_stats.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/mFILE.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/open_trace_file.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/pooled_alloc.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: cram/string_alloc.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/arith_dynamic.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/fqzcomp_qual.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/htscodecs.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/pack.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static4x16pr.o] Error 127 (ignored) 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 make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static32x16pr_avx2.o] Error 127 (ignored) 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 make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static32x16pr_avx512.o] Error 127 (ignored) 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 make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static32x16pr_sse4.o] Error 127 (ignored) 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 make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static32x16pr_neon.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static32x16pr.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rANS_static.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/rle.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/tokenise_name3.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: htscodecs/htscodecs/utils.o] Error 127 (ignored) fpic -fvisibility=hidden -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hfile_libcurl.o hfile_libcurl.c make[1]: fpic: No such file or directory make[1]: [Makefile.Rhtslib.win:160: hfile_libcurl.o] Error 127 (ignored) 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 make[1]: rc: No such file or directory make[1]: [Makefile.Rhtslib.win:317: libhts.a] Error 127 (ignored) libhts.a make[1]: libhts.a: No such file or directory make[1]: [Makefile.Rhtslib.win:318: libhts.a] Error 127 (ignored) make[1]: Leaving directory '/c/Users/GuoX/AppData/Local/Temp/RtmpEjLmGs/R.INSTALLa7003e625e3d/Rhtslib/src/htslib-1.18' mkdir -p "D:/Program Files/R/R-4.3.2/library/Rhtslib/usrlib/x64" cd "htslib-1.18" && cp libhts.a "D:/Program Files/R/R-4.3.2/library/Rhtslib/usrlib/x64" cp: cannot stat 'libhts.a': No such file or directory make: *** [Makevars.win:17: populate-usrlib-dir] Error 1 ERROR: compilation failed for package 'Rhtslib'
- removing 'D:/Program Files/R/R-4.3.2/library/Rhtslib' Warning in install.packages : 安装程序包‘E:/OneDrive/Publications/Rhtslib_3.0.0.tar.gz’时退出狀態的值不是0