Installing cutadapt on OS X

Question

[dugong]

Dear All,

I am trying to install cutadapt on OS X (Mavericks), Python 2.7.5. I tried all the options under readthedocs, nothing worked and did not find anything that gives me a clue how to fix it.

• pip keeps hanging

  pip install --user --upgrade cutadapt
  
  /Library/Python/2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
     InsecurePlatformWarning
     Using cached cutadapt-1.8.3.tar.gz
   Installing collected packages: cutadapt
     Running setup.py install for cutadapt
  

• manual installation keeps hanging

  python setup.py install --user
  running install
  running build
  running build_py
  running build_ext
  building 'cutadapt._align' extension
  cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cutadapt/_align.c -o build/temp.macosx-10.9-intel-2.7/cutadapt/_align.o
  cutadapt/_align.c:3732:21: warning: implicit conversion loses integer precision: 'Py_ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
  __pyx_v_self->m = __pyx_t_1;
                  ~ ^~~~~~~~~
  cutadapt/_align.c:4139:15: warning: implicit conversion loses integer precision: 'Py_ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
  __pyx_v_n = __pyx_t_5;
            ~ ^~~~~~~~~
  cutadapt/_align.c:4437:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    __pyx_v_min_n = __pyx_t_15;
                  ~ ^~~~~~~~~~
  cutadapt/_align.c:4583:44: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
      (__pyx_v_column[__pyx_v_i]).origin = __pyx_t_17;
                                         ~ ^~~~~~~~~~
  cutadapt/_align.c:4657:44: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
      (__pyx_v_column[__pyx_v_i]).origin = __pyx_t_14;
                                         ~ ^~~~~~~~~~
  cutadapt/_align.c:4898:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  __pyx_v_last = __pyx_t_14;
               ~ ^~~~~~~~~~
  cutadapt/_align.c:5507:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            __pyx_v_length = (__pyx_v_m + __pyx_t_17);
                           ~  ~~~~~~~~~~^~~~~~~~~~~~
  cutadapt/_align.c:5725:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    for (__pyx_t_13 = __pyx_v_first_i; __pyx_t_13 < __pyx_t_14; __pyx_t_13+=1) {
                    ~ ^~~~~~~~~~~~~~~
  cutadapt/_align.c:5742:35: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
      __pyx_v_length = (__pyx_v_i + __pyx_t_15);
                     ~  ~~~~~~~~~~^~~~~~~~~~~~
  cutadapt/_align.c:6463:15: warning: implicit conversion loses integer precision: 'Py_ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
  __pyx_v_m = __pyx_t_1;
            ~ ^~~~~~~~~
  cutadapt/_align.c:6473:15: warning: implicit conversion loses integer precision: 'Py_ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
  __pyx_v_n = __pyx_t_1;
            ~ ^~~~~~~~~- [I tried installing older versions too](http://wiki.bits.vib.be/index.php/Cutadapt)
  
  11 warnings generated.
  
  #### and it hangs here until ^C
  

• I tried installing from Github

• I tried installing older Versions

Answer 1

[ebrown1955]

Did you try easy install instead?

sudo easy_install cutadapt

[dugong]

Processing cutadapt
Writing .../cutadapt/setup.cfg
Running setup.py -q bdist_egg --dist-dir /Users/abelvertesy/cutadapt/egg-dist-tmp-6YXf0S
warning: no files found matching 'cutadapt/_align.so'
warning: no files found matching 'cutadapt/_qualtrim.so'
warning: no files found matching 'cutadapt/_seqio.so'

and keeps hanging

Answer 2

[John]

You should definitely try again using an up-to-date version of python. CPython 2.7.5 was released in May 2013 and doesn't support https which is why you're getting that urllib2 error. Maybe the other errors will go away if you update too.

I dont know what the -DENABLE_DTRACE flag is, but i know DTrace no longer works on OSX 10.11 (if thats what you are running). Although I doubt thats the reason you can't compile...

The best method to get this up-and-running as soon as possible is to install the Anaconda package, which will keep all your stuff up to date, and won't mess with the system version of Python. If it doesn't run on Anaconda, I would be surprised..

EDIT: And for what its worth, I just installed cutadapt on CPython 2.7.10 via pip and it took a few seconds to successfully install, although I have DTrace enabled on my system.

Second Edit: I turned on DTrace restrictions and it still installed via pip. I think you just need the latest python and XCode, and you should be fine.

Answer 3

[andrew.j.skelton73]

I'm not sure of this, but have you tried installing it through homebrew? brew install cutadapt

Answer 4

[dugong]

Hello Guys, thanks for the help!

@John: it still keeps hanging

Python 2.7.10 (v2.7.10:15c95b7d81dc, May 23 2015, 09:33:12)

pip install --user --upgrade cutadapt

Collecting cutadapt
  Using cached cutadapt-1.8.3.tar.gz
Installing collected packages: cutadapt
  Running setup.py install for cutadapt

....hangs until ^C

@ago by andrew.j.skelton73:

brew install cutadapt
Error: No available formula for cutadapt
Searching taps...

[John]

Hm....

Did you try upgrading XCode and command line tools? That's the only piece of the puzzle left that I can think of...