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
Did you try easy install instead?
sudo easy_install cutadapt
•
written
by
ebrown1955
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
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.
I'm not sure of this, but have you tried installing it through homebrew? brew install cutadapt
•
written
by
andrew.j.skelton73
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...
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