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zhonghua-wang / autocnv

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Fail to install in codespace #3

Open tyf111111 opened 10 months ago

tyf111111 commented 10 months ago

Fail to install with command pip install -r requirements.txt

Collecting pandas~=1.2.5 (from -r requirements.txt (line 1))
  Using cached pandas-1.2.5.tar.gz (5.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pyfaidx (from -r requirements.txt (line 2))
  Downloading pyfaidx-0.8.0-py3-none-any.whl.metadata (25 kB)
Collecting pysam~=0.16.0.1 (from -r requirements.txt (line 3))
  Downloading pysam-0.16.0.1.tar.gz (3.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 28.9 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [142 lines of output]
      # pysam: no cython available - using pre-compiled C
      # pysam: htslib mode is shared
      # pysam: HTSLIB_CONFIGURE_OPTIONS=None
      # pysam: (sysconfig) CC=gcc -pthread -B /home/codespace/miniconda3/compiler_compat
      # pysam: (sysconfig) CFLAGS=-DNDEBUG -fwrapv -O2 -Wall   -fPIC   -O2 -isystem /home/codespace/miniconda3/include -fPIC -O2   -isystem /home/codespace/miniconda3/include
      # pysam: (sysconfig) LDFLAGS=-Wl,-rpath,/home/codespace/miniconda3/lib -Wl,-rpath-link,/home/codespace/miniconda3/lib -L/home/codespace/miniconda3/lib -Wl,-rpath,/home/codespace/miniconda3/lib -Wl,-rpath-link,/home/codespace/miniconda3/lib -L/home/codespace/miniconda3/lib
      checking for gcc... gcc -pthread -B /home/codespace/miniconda3/compiler_compat
      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 -pthread -B /home/codespace/miniconda3/compiler_compat accepts -g... yes
      checking for gcc -pthread -B /home/codespace/miniconda3/compiler_compat 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... unknown
      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 compiler accepts -fvisibility=hidden... yes
      checking how to run the C preprocessor... gcc -pthread -B /home/codespace/miniconda3/compiler_compat -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 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 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 for libdeflate.h... no
      checking for libdeflate_deflate_compress in -ldeflate... no
      checking for curl_easy_pause in -lcurl... no
      checking for curl_easy_init in -lcurl... no
      configure: error: libcurl library not found

      Support for HTTPS and other SSL-based URLs requires routines from the libcurl
      library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
      requires libcurl development files to be installed on the build machine; you
      may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
      Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
      or Cygwin) is installed.

      Either configure with --disable-libcurl or resolve this error to build HTSlib.
      checking for gcc... gcc -pthread -B /home/codespace/miniconda3/compiler_compat
      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 -pthread -B /home/codespace/miniconda3/compiler_compat accepts -g... yes
      checking for gcc -pthread -B /home/codespace/miniconda3/compiler_compat 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... unknown
      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 compiler accepts -fvisibility=hidden... yes
      checking how to run the C preprocessor... gcc -pthread -B /home/codespace/miniconda3/compiler_compat -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 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 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 for libdeflate.h... no
      checking for libdeflate_deflate_compress in -ldeflate... no
      configure: WARNING: GCS support not enabled: requires libcurl support
      configure: WARNING: S3 support not enabled: requires libcurl support
      checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
      configure: creating ./config.status
      config.status: creating config.mk
      config.status: creating htslib.pc.tmp
      config.status: creating config.h
      make: ./version.sh: Command not found
      make: ./version.sh: Command not found
      error in pysam setup command: use_2to3 is invalid.
      # pysam: htslib configure options: --disable-libcurl
      # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.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_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o
      # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
      # pysam: htslib_config PLATFORM=default
      # pysam: config_option: ENABLE_GCS=0
      # pysam: config_option: ENABLE_PLUGINS=0
      # pysam: config_option: ENABLE_S3=0
      # pysam: config_option: HAVE_COMMONCRYPTO=0
      # pysam: config_option: HAVE_HMAC=0
      # pysam: config_option: HAVE_LIBBZ2=1
      # pysam: config_option: HAVE_LIBCURL=0
      # pysam: config_option: HAVE_LIBDEFLATE=0
      # pysam: config_option: HAVE_LIBLZMA=1
      # pysam: config_option: HAVE_MMAP=1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Mraderson commented 8 months ago

Could you please show me how to solve this