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Cannot upgrade cutadapt from 3.2 to 3.3

See original GitHub issue

Hello again, I currently have cutadapt 3.2 intalled with Python 3.6.9. I tried to upgrade to the latest version but the pip installer crashed. The reason seems to be in the isal dependency. No clue how to fix it.

fossandon@ubuntu:~/Documents/Github_repos/cutadapt$ pip3 install --upgrade cutadapt
Collecting cutadapt
  Using cached https://files.pythonhosted.org/packages/61/2a/33c9084f6f30417bf0561ee4c358c453c3bd3738c8cb14826e7956c1c299/cutadapt-3.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting xopen~=1.1.0 (from cutadapt)
  Using cached https://files.pythonhosted.org/packages/fd/4a/8721495b3681c87251711a8fe0c7b0faa3620dee9096fd3458fc1b50b81f/xopen-1.1.0-py2.py3-none-any.whl
Collecting dnaio~=0.5.0 (from cutadapt)
  Using cached https://files.pythonhosted.org/packages/1e/97/9f0b5e894e2ba89c71d7008e01c592bf18192850b83e60aa161fe2f1bb92/dnaio-0.5.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting dataclasses>=0.8; python_version < "3.7" (from cutadapt)
  Using cached https://files.pythonhosted.org/packages/fe/ca/75fac5856ab5cfa51bbbcefa250182e50441074fdc3f803f6e76451fab43/dataclasses-0.8-py3-none-any.whl
Collecting isal>=0.3.0; sys_platform == "linux" and platform_python_implementation != "PyPy" (from xopen~=1.1.0->cutadapt)
  Using cached https://files.pythonhosted.org/packages/e3/c0/2c3ebb4ea69186c58cf3ebe4c0c3e9683a19cf6da5f2f26010b31209d897/isal-0.5.0.tar.gz
Building wheels for collected packages: isal
  Running setup.py bdist_wheel for isal ... error
  Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-c3bxqhzd/isal/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpk1quul58pip-wheel- --python-tag cp36:
  /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'
    warnings.warn(msg)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/isal
  copying src/isal/igzip.py -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/__init__.py -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/version.pxd -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/__init__.pxd -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/crc.pxd -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/igzip_lib.pxd -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/isal_zlib.pyx -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/_isal.pyx -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/_isal.pyi -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/isal_zlib.pyi -> build/lib.linux-x86_64-3.6/isal
  copying src/isal/py.typed -> build/lib.linux-x86_64-3.6/isal
  creating build/lib.linux-x86_64-3.6/isal/isa-l
  copying src/isal/isa-l/LICENSE -> build/lib.linux-x86_64-3.6/isal/isa-l
  copying src/isal/isa-l/README.md -> build/lib.linux-x86_64-3.6/isal/isa-l
  copying src/isal/isa-l/Release_notes.txt -> build/lib.linux-x86_64-3.6/isal/isa-l
  running build_ext
  cythoning src/isal/isal_zlib.pyx to src/isal/isal_zlib.c
  cythoning src/isal/_isal.pyx to src/isal/_isal.c
  libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
  libtoolize: linking file 'build-aux/ltmain.sh'
  libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
  libtoolize: and rerunning libtoolize and aclocal.
  libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
  configure.ac:23: installing 'build-aux/compile'
  configure.ac:25: installing 'build-aux/config.guess'
  configure.ac:25: installing 'build-aux/config.sub'
  configure.ac:12: installing 'build-aux/install-sh'
  configure.ac:12: installing 'build-aux/missing'
  Makefile.am: installing 'build-aux/depcomp'
  parallel-tests: installing 'build-aux/test-driver'
  
  ----------------------------------------------------------------
  Initialized build system. For a common configuration please run:
  ----------------------------------------------------------------
  
  ./configure --prefix=/usr --libdir=/usr/lib
  
  checking for a BSD-compatible install... /usr/bin/install -c
  checking whether build environment is sane... yes
  checking for a thread-safe mkdir -p... /bin/mkdir -p
  checking for gawk... no
  checking for mawk... mawk
  checking whether make sets $(MAKE)... yes
  checking whether make supports nested variables... yes
  checking how to create a pax tar archive... gnutar
  checking for style of include used by make... GNU
  checking for gcc... gcc
  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 accepts -g... yes
  checking for gcc option to accept ISO C89... none needed
  checking whether gcc understands -c and -o together... yes
  checking dependency style of gcc... gcc3
  checking dependency style of gcc... gcc3
  checking build system type... x86_64-pc-linux-gnu
  checking host system type... x86_64-pc-linux-gnu
  checking for gcc option to accept ISO C99... none needed
  checking for gcc option to accept ISO Standard C... (cached) none needed
  checking for a sed that does not truncate output... /bin/sed
  checking for grep that handles long lines and -e... /bin/grep
  checking for egrep... /bin/grep -E
  checking for fgrep... /bin/grep -F
  checking how to print strings... printf
  checking for ld used by gcc... /usr/bin/ld
  checking if the linker (/usr/bin/ld) is GNU ld... yes
  checking how to run the C preprocessor... gcc -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 minix/config.h usability... no
  checking minix/config.h presence... no
  checking for minix/config.h... no
  checking whether it is safe to define __EXTENSIONS__... yes
  checking whether make supports nested variables... (cached) yes
  checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
  checking the name lister (/usr/bin/nm -B) interface... BSD nm
  checking whether ln -s works... yes
  checking the maximum length of command line arguments... 1572864
  checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
  checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
  checking for /usr/bin/ld option to reload object files... -r
  checking for objdump... objdump
  checking how to recognize dependent libraries... pass_all
  checking for dlltool... no
  checking how to associate runtime and link libraries... printf %s\n
  checking for ar... ar
  checking for archiver @FILE support... @
  checking for strip... strip
  checking for ranlib... ranlib
  checking command to parse /usr/bin/nm -B output from gcc object... ok
  checking for sysroot... no
  checking for a working dd... /bin/dd
  checking how to truncate binary pipes... /bin/dd bs=4096 count=1
  checking for mt... mt
  checking if mt is a manifest tool... no
  checking for dlfcn.h... yes
  checking for objdir... .libs
  checking if gcc supports -fno-rtti -fno-exceptions... no
  checking for gcc option to produce PIC... -fPIC -DPIC
  checking if gcc PIC flag -fPIC -DPIC works... yes
  checking if gcc static flag -static works... yes
  checking if gcc supports -c -o file.o... yes
  checking if gcc supports -c -o file.o... (cached) yes
  checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  checking whether -lc should be explicitly linked in... no
  checking dynamic linker characteristics... GNU/Linux ld.so
  checking how to hardcode library paths into programs... immediate
  checking whether stripping libraries is possible... yes
  checking if libtool supports shared libraries... yes
  checking whether to build shared libraries... yes
  checking whether to build static libraries... yes
  checking for a sed that does not truncate output... (cached) /bin/sed
  checking whether Intel CET is enabled... no
  checking for yasm... no
  no yasm
  checking for nasm... no
  no nasm
  configure: error: No modern nasm or yasm found as required. Nasm should be v2.11.01 or later (v2.13 for AVX512) and yasm should be 1.2.0 or later.
  make: *** No se especificó ningún objetivo y no se encontró ningún makefile.  Alto.
  make: *** No hay ninguna regla para construir el objetivo 'install'.  Alto.
  building 'isal.isal_zlib' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/src
  creating build/temp.linux-x86_64-3.6/src/isal
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/tmpl_q0e37_/include -I/usr/include/python3.6m -c src/isal/isal_zlib.c -o build/temp.linux-x86_64-3.6/src/isal/isal_zlib.o -fPIC
  src/isal/isal_zlib.c:604:10: fatal error: isa-l/crc.h: No existe el archivo o el directorio
   #include <isa-l/crc.h>
            ^~~~~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  
  ----------------------------------------
  Failed building wheel for isal
  Running setup.py clean for isal
Failed to build isal
Installing collected packages: isal, xopen, dnaio, dataclasses, cutadapt
  Running setup.py install for isal ... error
    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-c3bxqhzd/isal/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-h3x520ml-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
    /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'
      warnings.warn(msg)
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/isal
    copying src/isal/igzip.py -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/__init__.py -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/version.pxd -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/__init__.pxd -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/crc.pxd -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/igzip_lib.pxd -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/isal_zlib.pyx -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/_isal.pyx -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/_isal.pyi -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/isal_zlib.pyi -> build/lib.linux-x86_64-3.6/isal
    copying src/isal/py.typed -> build/lib.linux-x86_64-3.6/isal
    creating build/lib.linux-x86_64-3.6/isal/isa-l
    copying src/isal/isa-l/LICENSE -> build/lib.linux-x86_64-3.6/isal/isa-l
    copying src/isal/isa-l/README.md -> build/lib.linux-x86_64-3.6/isal/isa-l
    copying src/isal/isa-l/Release_notes.txt -> build/lib.linux-x86_64-3.6/isal/isa-l
    running build_ext
    skipping 'src/isal/isal_zlib.c' Cython extension (up-to-date)
    skipping 'src/isal/_isal.c' Cython extension (up-to-date)
    libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
    libtoolize: linking file 'build-aux/ltmain.sh'
    libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
    libtoolize: and rerunning libtoolize and aclocal.
    libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
    configure.ac:23: installing 'build-aux/compile'
    configure.ac:25: installing 'build-aux/config.guess'
    configure.ac:25: installing 'build-aux/config.sub'
    configure.ac:12: installing 'build-aux/install-sh'
    configure.ac:12: installing 'build-aux/missing'
    Makefile.am: installing 'build-aux/depcomp'
    parallel-tests: installing 'build-aux/test-driver'
    
    ----------------------------------------------------------------
    Initialized build system. For a common configuration please run:
    ----------------------------------------------------------------
    
    ./configure --prefix=/usr --libdir=/usr/lib
    
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... no
    checking for mawk... mawk
    checking whether make sets $(MAKE)... yes
    checking whether make supports nested variables... yes
    checking how to create a pax tar archive... gnutar
    checking for style of include used by make... GNU
    checking for gcc... gcc
    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 accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking whether gcc understands -c and -o together... yes
    checking dependency style of gcc... gcc3
    checking dependency style of gcc... gcc3
    checking build system type... x86_64-pc-linux-gnu
    checking host system type... x86_64-pc-linux-gnu
    checking for gcc option to accept ISO C99... none needed
    checking for gcc option to accept ISO Standard C... (cached) none needed
    checking for a sed that does not truncate output... /bin/sed
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for fgrep... /bin/grep -F
    checking how to print strings... printf
    checking for ld used by gcc... /usr/bin/ld
    checking if the linker (/usr/bin/ld) is GNU ld... yes
    checking how to run the C preprocessor... gcc -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 minix/config.h usability... no
    checking minix/config.h presence... no
    checking for minix/config.h... no
    checking whether it is safe to define __EXTENSIONS__... yes
    checking whether make supports nested variables... (cached) yes
    checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
    checking the name lister (/usr/bin/nm -B) interface... BSD nm
    checking whether ln -s works... yes
    checking the maximum length of command line arguments... 1572864
    checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
    checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
    checking for /usr/bin/ld option to reload object files... -r
    checking for objdump... objdump
    checking how to recognize dependent libraries... pass_all
    checking for dlltool... no
    checking how to associate runtime and link libraries... printf %s\n
    checking for ar... ar
    checking for archiver @FILE support... @
    checking for strip... strip
    checking for ranlib... ranlib
    checking command to parse /usr/bin/nm -B output from gcc object... ok
    checking for sysroot... no
    checking for a working dd... /bin/dd
    checking how to truncate binary pipes... /bin/dd bs=4096 count=1
    checking for mt... mt
    checking if mt is a manifest tool... no
    checking for dlfcn.h... yes
    checking for objdir... .libs
    checking if gcc supports -fno-rtti -fno-exceptions... no
    checking for gcc option to produce PIC... -fPIC -DPIC
    checking if gcc PIC flag -fPIC -DPIC works... yes
    checking if gcc static flag -static works... yes
    checking if gcc supports -c -o file.o... yes
    checking if gcc supports -c -o file.o... (cached) yes
    checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
    checking whether -lc should be explicitly linked in... no
    checking dynamic linker characteristics... GNU/Linux ld.so
    checking how to hardcode library paths into programs... immediate
    checking whether stripping libraries is possible... yes
    checking if libtool supports shared libraries... yes
    checking whether to build shared libraries... yes
    checking whether to build static libraries... yes
    checking for a sed that does not truncate output... (cached) /bin/sed
    checking whether Intel CET is enabled... no
    checking for yasm... no
    no yasm
    checking for nasm... no
    no nasm
    configure: error: No modern nasm or yasm found as required. Nasm should be v2.11.01 or later (v2.13 for AVX512) and yasm should be 1.2.0 or later.
    make: *** No se especificó ningún objetivo y no se encontró ningún makefile.  Alto.
    make: *** No hay ninguna regla para construir el objetivo 'install'.  Alto.
    building 'isal.isal_zlib' extension
    creating build/temp.linux-x86_64-3.6
    creating build/temp.linux-x86_64-3.6/src
    creating build/temp.linux-x86_64-3.6/src/isal
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/tmpukrtly_2/include -I/usr/include/python3.6m -c src/isal/isal_zlib.c -o build/temp.linux-x86_64-3.6/src/isal/isal_zlib.o -fPIC
    src/isal/isal_zlib.c:604:10: fatal error: isa-l/crc.h: No existe el archivo o el directorio
     #include <isa-l/crc.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-c3bxqhzd/isal/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-h3x520ml-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-c3bxqhzd/isal/
fossandon@ubuntu:~/Documents/Github_repos/cutadapt$

Issue Analytics

State:
Created 3 years ago
Comments:8 (5 by maintainers)

Top GitHub Comments

1reaction

marcelmcommented, Mar 10, 2021

Yes, that’s quite an old pip version 😃. Glad I could help!

1reaction

fjossandoncommented, Mar 9, 2021

My pip version is: pip 9.0.1 from /usr/lib/python3/dist-packages (python 3.6), so I made the upgrade:

fossandon@ubuntu:~/Documents/Github_repos/cutadapt$ pip3 install --upgrade pip
Collecting pip
  Cache entry deserialization failed, entry ignored
  Downloading https://files.pythonhosted.org/packages/fe/ef/60d7ba03b5c442309ef42e7d69959f73aacccd0d86008362a681c4698e83/pip-21.0.1-py3-none-any.whl (1.5MB)
    100% |████████████████████████████████| 1.5MB 927kB/s 
Installing collected packages: pip
Successfully installed pip-21.0.1

After that I tried again and it worked!

fossandon@ubuntu:~/Documents/Github_repos/cutadapt$ pip3 install cutadapt==3.3
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Defaulting to user installation because normal site-packages is not writeable
Collecting cutadapt==3.3
  Using cached cutadapt-3.3-cp36-cp36m-manylinux1_x86_64.whl (146 kB)
Requirement already satisfied: dataclasses>=0.8 in /home/fossandon/.local/lib/python3.6/site-packages (from cutadapt==3.3) (0.8)
Collecting xopen~=1.1.0
  Using cached xopen-1.1.0-py2.py3-none-any.whl (10 kB)
Requirement already satisfied: dnaio~=0.5.0 in /home/fossandon/.local/lib/python3.6/site-packages (from cutadapt==3.3) (0.5.0)
Collecting isal>=0.3.0
  Downloading isal-0.5.0-cp36-cp36m-manylinux2014_x86_64.whl (391 kB)
     |████████████████████████████████| 391 kB 530 kB/s 
Installing collected packages: isal, xopen, cutadapt
  Attempting uninstall: xopen
    Found existing installation: xopen 1.0.1
    Uninstalling xopen-1.0.1:
      Successfully uninstalled xopen-1.0.1
  Attempting uninstall: cutadapt
    Found existing installation: cutadapt 3.2
    Uninstalling cutadapt-3.2:
      Successfully uninstalled cutadapt-3.2
Successfully installed cutadapt-3.3 isal-0.5.0 xopen-1.1.0
fossandon@ubuntu:~/Documents/Github_repos/cutadapt$

Thanks for the all the help. =)

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