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/