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XiaoTaoWang / HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies
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error occured when install hic-straw #5

Open wbszhu opened 1 year ago

wbszhu commented 1 year ago

Hi, for some reason, I have to reinstall pairLiftOver. And meet the error like this. conda create -n tmp_pairliftover cooler pairtools kerneltree

conda activate tmp_pairliftover

pip install pairLiftOver hic-straw

Collecting pairLiftOver
  Using cached pairLiftOver-0.2.1-py3-none-any.whl (27.8 MB)
Collecting hic-straw
  Using cached hic-straw-1.3.1.tar.gz (18 kB)
  Preparing metadata (setup.py) ... done
Collecting pybind11>=2.4
  Using cached pybind11-2.10.1-py3-none-any.whl (216 kB)
Building wheels for collected packages: hic-straw
  Building wheel for hic-straw (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [151 lines of output]
      /public/home/luzhang/miniconda3/envs/tmp_pairliftover/lib/python3.9/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
        warnings.warn(
      running bdist_wheel
      running build
      running build_ext
      creating tmp
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c /tmp/tmptd2jpyrt.cpp -o tmp/tmptd2jpyrt.o -std=c++14
      gcc: error: unrecognized command line option ‘-std=c++14’
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c /tmp/tmpa_6i3pmp.cpp -o tmp/tmpa_6i3pmp.o -std=c++11
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c /tmp/tmpr0wktmip.cpp -o tmp/tmpr0wktmip.o -fvisibility=hidden
      building 'hicstraw' extension
      creating build
      creating build/temp.linux-x86_64-cpython-39
      creating build/temp.linux-x86_64-cpython-39/src
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/tmp/pip-install-9vcbitof/hic-straw_448ceb0f986045b7bca6d29f1fc5545a/.eggs/pybind11-2.10.1-py3.9.egg/pybind11/include -I/tmp/pip-install-9vcbitof/hic-straw_448ceb0f986045b7bca6d29f1fc5545a/.eggs/pybind11-2.10.1-py3.9.egg/pybind11/include -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c src/straw.cpp -o build/temp.linux-x86_64-cpython-39/src/straw.o -DVERSION_INFO=\"1.3.1\" -std=c++11 -fvisibility=hidden
      src/straw.cpp: In function ‘bool readFooterURL(CURL*, int64_t, int32_t, int32_t, int32_t, const string&, const string&, const string&, int32_t, int64_t&, indexEntry&, indexEntry&, std::vector<double>&)’:
      src/straw.cpp:464:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int64_t nBytes = readInt64FromFile(fin);
                       ^
      src/straw.cpp:467:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int32_t nBytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp:481:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, bufferSize0);
               ^
      In file included from src/straw.cpp:38:0:
      src/straw.h:60:8: note: ‘memstream& memstream::operator=(memstream&&)’ is implicitly deleted because the default definition would be ill-formed:
       struct memstream : virtual membuf, std::istream {
              ^
      src/straw.h:60:8: error: use of deleted function ‘membuf& membuf::operator=(membuf&&)’
      src/straw.h:54:8: note: ‘membuf& membuf::operator=(membuf&&)’ is implicitly deleted because the default definition would be ill-formed:
       struct membuf : std::streambuf {
              ^
      In file included from /usr/include/c++/4.8.2/ios:43:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private
             operator=(const basic_streambuf& __sb)
             ^
      In file included from src/straw.cpp:38:0:
      src/straw.h:54:8: error: within this context
       struct membuf : std::streambuf {
              ^
      src/straw.h:60:8: error: use of deleted function ‘std::basic_istream<char>& std::basic_istream<char>::operator=(const std::basic_istream<char>&)’
       struct memstream : virtual membuf, std::istream {
              ^
      In file included from /usr/include/c++/4.8.2/iostream:40:0,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/istream:58:11: note: ‘std::basic_istream<char>& std::basic_istream<char>::operator=(const std::basic_istream<char>&)’ is implicitly deleted because the default definition would be ill-formed:
           class basic_istream : virtual public basic_ios<_CharT, _Traits>
                 ^
      /usr/include/c++/4.8.2/istream:58:11: error: use of deleted function ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’
      In file included from /usr/include/c++/4.8.2/ios:44:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/bits/basic_ios.h:66:11: note: ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’ is implicitly deleted because the default definition would be ill-formed:
           class basic_ios : public ios_base
                 ^
      In file included from /usr/include/c++/4.8.2/ios:42:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/bits/ios_base.h:789:5: error: ‘std::ios_base& std::ios_base::operator=(const std::ios_base&)’ is private
           operator=(const ios_base&);
           ^
      In file included from /usr/include/c++/4.8.2/ios:44:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/bits/basic_ios.h:66:11: error: within this context
           class basic_ios : public ios_base
                 ^
      src/straw.cpp:489:17: warning: unused variable ‘sizeinbytes’ [-Wunused-variable]
               int32_t sizeinbytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp:509:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, 100);
               ^
      src/straw.cpp:517:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 1000);
                   ^
      src/straw.cpp:542:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 100);
                   ^
      src/straw.cpp:559:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, 100);
               ^
      src/straw.cpp:565:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 1000);
                   ^
      src/straw.cpp:590:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 100);
                   ^
      src/straw.cpp:606:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, 100);
               ^
      src/straw.cpp:615:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, bufferSize2);
               ^
      src/straw.cpp: In function ‘bool readFooter(std::istream&, int64_t, int32_t, int32_t, int32_t, const string&, const string&, const string&, int32_t, int64_t&, indexEntry&, indexEntry&, std::vector<double>&)’:
      src/straw.cpp:663:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int64_t nBytes = readInt64FromFile(fin);
                       ^
      src/straw.cpp:665:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int32_t nBytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp:678:17: warning: unused variable ‘sizeinbytes’ [-Wunused-variable]
               int32_t sizeinbytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp: In function ‘std::map<int, indexEntry> readMatrixHttp(CURL*, int64_t, const string&, int32_t, float&, int32_t&, int32_t&)’:
      src/straw.cpp:881:13: warning: unused variable ‘c1’ [-Wunused-variable]
           int32_t c1 = readInt32FromFile(bufin);
                   ^
      src/straw.cpp:882:13: warning: unused variable ‘c2’ [-Wunused-variable]
           int32_t c2 = readInt32FromFile(bufin);
                   ^
      src/straw.cpp: In function ‘std::map<int, indexEntry> readMatrix(std::istream&, int64_t, const string&, int32_t, float&, int32_t&, int32_t&)’:
      src/straw.cpp:909:13: warning: unused variable ‘c1’ [-Wunused-variable]
           int32_t c1 = readInt32FromFile(fin);
                   ^
      src/straw.cpp:910:13: warning: unused variable ‘c2’ [-Wunused-variable]
           int32_t c2 = readInt32FromFile(fin);
                   ^
      src/straw.cpp: At global scope:
      src/straw.cpp:1304:37: warning: ‘getNormVector’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
           auto getNormVector(int32_t index) {
                                           ^
      src/straw.cpp:1316:28: warning: ‘getExpectedValues’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
           auto getExpectedValues() {
                                  ^
      src/straw.cpp:1381:79: warning: ‘getRecordsAsMatrix’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
           auto getRecordsAsMatrix(int64_t gx0, int64_t gx1, int64_t gy0, int64_t gy1) {
                                                                                     ^
      src/straw.cpp: In member function ‘std::vector<chromosome> HiCFile::getChromosomes()’:
      src/straw.cpp:1536:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               for(int32_t i = 0; i < chromosomeMap.size(); i++){
                                                         ^
      src/straw.cpp: At global scope:
      src/straw.cpp:1597:78: warning: ‘strawAsMatrix’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
                          const string &chr2loc, const string &unit, int32_t binsize) {
                                                                                    ^
      src/straw.cpp: In function ‘int64_t getNumRecordsForFile(const string&, int32_t, bool)’:
      src/straw.cpp:1631:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(int32_t i = 0; i < chromosomes.size(); i++){
                                                   ^
      src/straw.cpp:1633:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               for(int32_t j = i + indexOffset; j < chromosomes.size(); j++){
                                                                     ^
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for hic-straw
  Running setup.py clean for hic-straw
Failed to build hic-straw
Installing collected packages: pairLiftOver, pybind11, hic-straw
  Running setup.py install for hic-straw ... error
  error: subprocess-exited-with-error

  × Running setup.py install for hic-straw did not run successfully.
  │ exit code: 1
  ╰─> [150 lines of output]
      running install
      /public/home/luzhang/miniconda3/envs/tmp_pairliftover/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      running build_ext
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c /tmp/tmp8e9sw1w8.cpp -o tmp/tmp8e9sw1w8.o -std=c++14
      gcc: error: unrecognized command line option ‘-std=c++14’
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c /tmp/tmpqf5u9the.cpp -o tmp/tmpqf5u9the.o -std=c++11
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c /tmp/tmp_lwlscij.cpp -o tmp/tmp_lwlscij.o -fvisibility=hidden
      building 'hicstraw' extension
      creating build
      creating build/temp.linux-x86_64-cpython-39
      creating build/temp.linux-x86_64-cpython-39/src
      gcc -pthread -B /public/home/luzhang/miniconda3/envs/tmp_pairliftover/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -O2 -isystem /public/home/luzhang/miniconda3/envs/tmp_pairliftover/include -fPIC -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/lib/python3.9/site-packages/pybind11/include -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/lib/python3.9/site-packages/pybind11/include -I/public/home/luzhang/miniconda3/envs/tmp_pairliftover/include/python3.9 -c src/straw.cpp -o build/temp.linux-x86_64-cpython-39/src/straw.o -DVERSION_INFO=\"1.3.1\" -std=c++11 -fvisibility=hidden
      src/straw.cpp: In function ‘bool readFooterURL(CURL*, int64_t, int32_t, int32_t, int32_t, const string&, const string&, const string&, int32_t, int64_t&, indexEntry&, indexEntry&, std::vector<double>&)’:
      src/straw.cpp:464:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int64_t nBytes = readInt64FromFile(fin);
                       ^
      src/straw.cpp:467:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int32_t nBytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp:481:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, bufferSize0);
               ^
      In file included from src/straw.cpp:38:0:
      src/straw.h:60:8: note: ‘memstream& memstream::operator=(memstream&&)’ is implicitly deleted because the default definition would be ill-formed:
       struct memstream : virtual membuf, std::istream {
              ^
      src/straw.h:60:8: error: use of deleted function ‘membuf& membuf::operator=(membuf&&)’
      src/straw.h:54:8: note: ‘membuf& membuf::operator=(membuf&&)’ is implicitly deleted because the default definition would be ill-formed:
       struct membuf : std::streambuf {
              ^
      In file included from /usr/include/c++/4.8.2/ios:43:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private
             operator=(const basic_streambuf& __sb)
             ^
      In file included from src/straw.cpp:38:0:
      src/straw.h:54:8: error: within this context
       struct membuf : std::streambuf {
              ^
      src/straw.h:60:8: error: use of deleted function ‘std::basic_istream<char>& std::basic_istream<char>::operator=(const std::basic_istream<char>&)’
       struct memstream : virtual membuf, std::istream {
              ^
      In file included from /usr/include/c++/4.8.2/iostream:40:0,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/istream:58:11: note: ‘std::basic_istream<char>& std::basic_istream<char>::operator=(const std::basic_istream<char>&)’ is implicitly deleted because the default definition would be ill-formed:
           class basic_istream : virtual public basic_ios<_CharT, _Traits>
                 ^
      /usr/include/c++/4.8.2/istream:58:11: error: use of deleted function ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’
      In file included from /usr/include/c++/4.8.2/ios:44:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/bits/basic_ios.h:66:11: note: ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’ is implicitly deleted because the default definition would be ill-formed:
           class basic_ios : public ios_base
                 ^
      In file included from /usr/include/c++/4.8.2/ios:42:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/bits/ios_base.h:789:5: error: ‘std::ios_base& std::ios_base::operator=(const std::ios_base&)’ is private
           operator=(const ios_base&);
           ^
      In file included from /usr/include/c++/4.8.2/ios:44:0,
                       from /usr/include/c++/4.8.2/ostream:38,
                       from /usr/include/c++/4.8.2/iostream:39,
                       from src/straw.cpp:25:
      /usr/include/c++/4.8.2/bits/basic_ios.h:66:11: error: within this context
           class basic_ios : public ios_base
                 ^
      src/straw.cpp:489:17: warning: unused variable ‘sizeinbytes’ [-Wunused-variable]
               int32_t sizeinbytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp:509:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, 100);
               ^
      src/straw.cpp:517:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 1000);
                   ^
      src/straw.cpp:542:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 100);
                   ^
      src/straw.cpp:559:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, 100);
               ^
      src/straw.cpp:565:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 1000);
                   ^
      src/straw.cpp:590:13: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
               fin = memstream(buffer, 100);
                   ^
      src/straw.cpp:606:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, 100);
               ^
      src/straw.cpp:615:9: error: use of deleted function ‘memstream& memstream::operator=(memstream&&)’
           fin = memstream(buffer, bufferSize2);
               ^
      src/straw.cpp: In function ‘bool readFooter(std::istream&, int64_t, int32_t, int32_t, int32_t, const string&, const string&, const string&, int32_t, int64_t&, indexEntry&, indexEntry&, std::vector<double>&)’:
      src/straw.cpp:663:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int64_t nBytes = readInt64FromFile(fin);
                       ^
      src/straw.cpp:665:17: warning: unused variable ‘nBytes’ [-Wunused-variable]
               int32_t nBytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp:678:17: warning: unused variable ‘sizeinbytes’ [-Wunused-variable]
               int32_t sizeinbytes = readInt32FromFile(fin);
                       ^
      src/straw.cpp: In function ‘std::map<int, indexEntry> readMatrixHttp(CURL*, int64_t, const string&, int32_t, float&, int32_t&, int32_t&)’:
      src/straw.cpp:881:13: warning: unused variable ‘c1’ [-Wunused-variable]
           int32_t c1 = readInt32FromFile(bufin);
                   ^
      src/straw.cpp:882:13: warning: unused variable ‘c2’ [-Wunused-variable]
           int32_t c2 = readInt32FromFile(bufin);
                   ^
      src/straw.cpp: In function ‘std::map<int, indexEntry> readMatrix(std::istream&, int64_t, const string&, int32_t, float&, int32_t&, int32_t&)’:
      src/straw.cpp:909:13: warning: unused variable ‘c1’ [-Wunused-variable]
           int32_t c1 = readInt32FromFile(fin);
                   ^
      src/straw.cpp:910:13: warning: unused variable ‘c2’ [-Wunused-variable]
           int32_t c2 = readInt32FromFile(fin);
                   ^
      src/straw.cpp: At global scope:
      src/straw.cpp:1304:37: warning: ‘getNormVector’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
           auto getNormVector(int32_t index) {
                                           ^
      src/straw.cpp:1316:28: warning: ‘getExpectedValues’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
           auto getExpectedValues() {
                                  ^
      src/straw.cpp:1381:79: warning: ‘getRecordsAsMatrix’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
           auto getRecordsAsMatrix(int64_t gx0, int64_t gx1, int64_t gy0, int64_t gy1) {
                                                                                     ^
      src/straw.cpp: In member function ‘std::vector<chromosome> HiCFile::getChromosomes()’:
      src/straw.cpp:1536:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               for(int32_t i = 0; i < chromosomeMap.size(); i++){
                                                         ^
      src/straw.cpp: At global scope:
      src/straw.cpp:1597:78: warning: ‘strawAsMatrix’ function uses ‘auto’ type specifier without trailing return type [enabled by default]
                          const string &chr2loc, const string &unit, int32_t binsize) {
                                                                                    ^
      src/straw.cpp: In function ‘int64_t getNumRecordsForFile(const string&, int32_t, bool)’:
      src/straw.cpp:1631:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           for(int32_t i = 0; i < chromosomes.size(); i++){
                                                   ^
      src/straw.cpp:1633:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
               for(int32_t j = i + indexOffset; j < chromosomes.size(); j++){
                                                                     ^
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> hic-straw

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Python 3.9.13 pairliftover 0.2.1

Thanks for your help.

XiaoTaoWang commented 1 year ago

Interesting ... I would suggest you installing c++ compiler before running pip:

$ conda activate tmp_pairliftover
$ conda install cxx-compiler
$ pip install pairLiftOver hic-straw

Let me know whether it works!

Xiaotao

wbszhu commented 1 year ago

Hi! I follow your recommend. It works, all things is ok. Thanks, Lu Zhang