Q2Studio Installation Problem, GCC error- Unable to build wheel for greenlet

User Support
1

I get this error after the pip install . command and then I am unable to go ahead with the rest of the installation. Any insight into how to rectify this is appreciated.

(qiime2-2018.6) Janielles-MacBook-Pro:q2studio-2018.6.0 jsvidal$ pip install .
Processing /Users/jsvidal/q2studio-2018.6.0
Requirement already satisfied: click in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from q2studio==2018.6.0) (6.7)
Requirement already satisfied: flask in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from q2studio==2018.6.0) (1.0.2)
Collecting gevent (from q2studio==2018.6.0)
Using cached https://files.pythonhosted.org/packages/ba/4a/68cc27925a231aeb68eac95b8cd7a18e0f6a997b51ecdabd5f42c5b1b78b/gevent-1.3.5-cp35-cp35m-macosx_10_6_intel.whl
Requirement already satisfied: qiime2==2018.6.* in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from q2studio==2018.6.0) (2018.6.0)
Requirement already satisfied: itsdangerous>=0.24 in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from flask->q2studio==2018.6.0) (0.24)
Requirement already satisfied: Jinja2>=2.10 in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from flask->q2studio==2018.6.0) (2.10)
Requirement already satisfied: Werkzeug>=0.14 in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from flask->q2studio==2018.6.0) (0.14.1)
Collecting greenlet>=0.4.13; platform_python_implementation == “CPython” (from gevent->q2studio==2018.6.0)
Using cached https://files.pythonhosted.org/packages/5d/82/2e53a8def6f99db51992ca3a0a2448c3bbec1a9db3a7cbf7d5dad011e138/greenlet-0.4.14.tar.gz
Requirement already satisfied: MarkupSafe>=0.23 in /Users/jsvidal/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages (from Jinja2>=2.10->flask->q2studio==2018.6.0) (1.0)
Building wheels for collected packages: q2studio, greenlet
Running setup.py bdist_wheel for q2studio … done
Stored in directory: /Users/jsvidal/Library/Caches/pip/wheels/a8/0b/b5/549bd081e5e53203d9d2e04d0b5b0bab3741d8a64740d33d92
Running setup.py bdist_wheel for greenlet … error
Complete output from command /Users/jsvidal/miniconda3/envs/qiime2-2018.6/bin/python -u -c “import setuptools, tokenize;file=’/private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-install-bpe8oqd0/greenlet/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 /private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-wheel-2bt5okjy --python-tag cp35:
running bdist_wheel
running build
running build_ext
building ‘greenlet’ extension
creating build
creating build/temp.macosx-10.9-x86_64-3.5
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/jsvidal/miniconda3/envs/qiime2-2018.6/include -arch x86_64 -I/Users/jsvidal/miniconda3/envs/qiime2-2018.6/include/python3.5m -c greenlet.c -o build/temp.macosx-10.9-x86_64-3.5/greenlet.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command ‘gcc’ failed with exit status 1

Failed building wheel for greenlet
Running setup.py clean for greenlet
Successfully built q2studio
Failed to build greenlet
Installing collected packages: greenlet, gevent, q2studio
Running setup.py install for greenlet … error
Complete output from command /Users/jsvidal/miniconda3/envs/qiime2-2018.6/bin/python -u -c “import setuptools, tokenize;file=’/private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-install-bpe8oqd0/greenlet/setup.py’;f=getattr(tokenize, ‘open’, open)(file);code=f.read().replace(’\r\n’, ‘\n’);f.close();exec(compile(code, file, ‘exec’))” install --record /private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-record-1511fkcg/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_ext
building ‘greenlet’ extension
creating build
creating build/temp.macosx-10.9-x86_64-3.5
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/jsvidal/miniconda3/envs/qiime2-2018.6/include -arch x86_64 -I/Users/jsvidal/miniconda3/envs/qiime2-2018.6/include/python3.5m -c greenlet.c -o build/temp.macosx-10.9-x86_64-3.5/greenlet.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command ‘gcc’ failed with exit status 1

----------------------------------------

Command “/Users/jsvidal/miniconda3/envs/qiime2-2018.6/bin/python -u -c “import setuptools, tokenize;file=’/private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-install-bpe8oqd0/greenlet/setup.py’;f=getattr(tokenize, ‘open’, open)(file);code=f.read().replace(’\r\n’, ‘\n’);f.close();exec(compile(code, file, ‘exec’))” install --record /private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-record-1511fkcg/install-record.txt --single-version-externally-managed --compile” failed with error code 1 in /private/var/folders/_9/j06jwfq55zlgslj8hz273lfw0000gn/T/pip-install-bpe8oqd0/greenlet/

3

Hey there @jsv!

The error has to do with your system's incomplete installation of xcode, apparently:

I am not too sure what to tell you, we don't work with the xcode toolkit at all so we don't have any experience there. Maybe try reinstalling xcode or updating it. You might also try uninstalling xcode, since gcc shouldn't be a requirement for any of this (it looks like since you have gcc in your PATH, pip is trying to use it to compile greenlet).

Keep us posted!

5

I’m a complete newbie to all of this and Python so I’m not even sure how I got here. How would I do what you suggested??

Thanks so much.

7

To be honest, I have no clue what is going on. Googling revealed this blog post (note item three):

as well as this:

A few high-level comments though:

Otherwise, if you want to install the studio natively, I think you should investigate getting xcode up and running correctly first, since that seems to be implicated in the error above (xcode isn't a requirement from our end, but since you have it on your computer it seems to be involved somehow). Keep us posted! :qiime2:

9

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