I was installing cryoSPARC under Ubuntu 16.04 and got the following error during the installation of Python packages:
----------------------------------------
Failed building wheel for pycrypto
Running setup.py clean for pycrypto
Failed to build pycrypto
Installing collected packages: pylbfgs, pyyaml, diskcache, pymongo, nvidia-ml-py, pycrypto, psutil
Running setup.py install for pycrypto ... error
Complete output from command /opt/cryosparc/anaconda2/bin/python -u -c "import setuptools, tokenize;__file__='/mnt/cache/scratch/pip-build-9pWjy0/pycrypto/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /mnt/cache/scratch/pip-VVqtwX-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/Crypto
copying lib/Crypto/pct_warnings.py -> build/lib.linux-x86_64-2.7/Crypto
copying lib/Crypto/__init__.py -> build/lib.linux-x86_64-2.7/Crypto
creating build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/MD4.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/RIPEMD.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/SHA512.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/SHA384.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/MD5.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/HMAC.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/hashalgo.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/SHA256.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/SHA224.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/SHA.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
copying lib/Crypto/Hash/MD2.py -> build/lib.linux-x86_64-2.7/Crypto/Hash
creating build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/DES.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/DES3.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/XOR.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/ARC4.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/CAST.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/PKCS1_v1_5.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/PKCS1_OAEP.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/blockalgo.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/Blowfish.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/AES.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
copying lib/Crypto/Cipher/ARC2.py -> build/lib.linux-x86_64-2.7/Crypto/Cipher
creating build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/randpool.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/py21compat.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/number.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/winrandom.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/Counter.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/asn1.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/RFC1751.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/_number_new.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Util
copying lib/Crypto/Util/py3compat.py -> build/lib.linux-x86_64-2.7/Crypto/Util
creating build/lib.linux-x86_64-2.7/Crypto/Random
copying lib/Crypto/Random/_UserFriendlyRNG.py -> build/lib.linux-x86_64-2.7/Crypto/Random
copying lib/Crypto/Random/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Random
copying lib/Crypto/Random/random.py -> build/lib.linux-x86_64-2.7/Crypto/Random
creating build/lib.linux-x86_64-2.7/Crypto/Random/Fortuna
copying lib/Crypto/Random/Fortuna/SHAd256.py -> build/lib.linux-x86_64-2.7/Crypto/Random/Fortuna
copying lib/Crypto/Random/Fortuna/FortunaGenerator.py -> build/lib.linux-x86_64-2.7/Crypto/Random/Fortuna
copying lib/Crypto/Random/Fortuna/FortunaAccumulator.py -> build/lib.linux-x86_64-2.7/Crypto/Random/Fortuna
copying lib/Crypto/Random/Fortuna/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Random/Fortuna
creating build/lib.linux-x86_64-2.7/Crypto/Random/OSRNG
copying lib/Crypto/Random/OSRNG/fallback.py -> build/lib.linux-x86_64-2.7/Crypto/Random/OSRNG
copying lib/Crypto/Random/OSRNG/rng_base.py -> build/lib.linux-x86_64-2.7/Crypto/Random/OSRNG
copying lib/Crypto/Random/OSRNG/nt.py -> build/lib.linux-x86_64-2.7/Crypto/Random/OSRNG
copying lib/Crypto/Random/OSRNG/posix.py -> build/lib.linux-x86_64-2.7/Crypto/Random/OSRNG
copying lib/Crypto/Random/OSRNG/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Random/OSRNG
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest
copying lib/Crypto/SelfTest/st_common.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest
copying lib/Crypto/SelfTest/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/common.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_DES.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_XOR.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_Blowfish.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_CAST.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_pkcs1_15.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_AES.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_DES3.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_ARC2.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_pkcs1_oaep.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
copying lib/Crypto/SelfTest/Cipher/test_ARC4.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Cipher
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/common.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_MD4.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_SHA512.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_HMAC.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_SHA.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_MD5.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_MD2.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_RIPEMD.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_SHA384.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_SHA224.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/test_SHA256.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
copying lib/Crypto/SelfTest/Hash/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Hash
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Protocol
copying lib/Crypto/SelfTest/Protocol/test_KDF.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Protocol
copying lib/Crypto/SelfTest/Protocol/test_chaffing.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Protocol
copying lib/Crypto/SelfTest/Protocol/test_rfc1751.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Protocol
copying lib/Crypto/SelfTest/Protocol/test_AllOrNothing.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Protocol
copying lib/Crypto/SelfTest/Protocol/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Protocol
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/PublicKey
copying lib/Crypto/SelfTest/PublicKey/test_ElGamal.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/PublicKey
copying lib/Crypto/SelfTest/PublicKey/test_RSA.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/PublicKey
copying lib/Crypto/SelfTest/PublicKey/test_importKey.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/PublicKey
copying lib/Crypto/SelfTest/PublicKey/test_DSA.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/PublicKey
copying lib/Crypto/SelfTest/PublicKey/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/PublicKey
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random
copying lib/Crypto/SelfTest/Random/test__UserFriendlyRNG.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random
copying lib/Crypto/SelfTest/Random/test_rpoolcompat.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random
copying lib/Crypto/SelfTest/Random/test_random.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random
copying lib/Crypto/SelfTest/Random/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/Fortuna
copying lib/Crypto/SelfTest/Random/Fortuna/test_SHAd256.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/Fortuna
copying lib/Crypto/SelfTest/Random/Fortuna/test_FortunaAccumulator.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/Fortuna
copying lib/Crypto/SelfTest/Random/Fortuna/test_FortunaGenerator.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/Fortuna
copying lib/Crypto/SelfTest/Random/Fortuna/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/Fortuna
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
copying lib/Crypto/SelfTest/Random/OSRNG/test_nt.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
copying lib/Crypto/SelfTest/Random/OSRNG/test_generic.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
copying lib/Crypto/SelfTest/Random/OSRNG/test_winrandom.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
copying lib/Crypto/SelfTest/Random/OSRNG/test_fallback.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
copying lib/Crypto/SelfTest/Random/OSRNG/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
copying lib/Crypto/SelfTest/Random/OSRNG/test_posix.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Random/OSRNG
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Util
copying lib/Crypto/SelfTest/Util/test_asn1.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Util
copying lib/Crypto/SelfTest/Util/test_Counter.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Util
copying lib/Crypto/SelfTest/Util/test_winrandom.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Util
copying lib/Crypto/SelfTest/Util/test_number.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Util
copying lib/Crypto/SelfTest/Util/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Util
creating build/lib.linux-x86_64-2.7/Crypto/SelfTest/Signature
copying lib/Crypto/SelfTest/Signature/test_pkcs1_pss.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Signature
copying lib/Crypto/SelfTest/Signature/test_pkcs1_15.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Signature
copying lib/Crypto/SelfTest/Signature/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/SelfTest/Signature
creating build/lib.linux-x86_64-2.7/Crypto/Protocol
copying lib/Crypto/Protocol/Chaffing.py -> build/lib.linux-x86_64-2.7/Crypto/Protocol
copying lib/Crypto/Protocol/AllOrNothing.py -> build/lib.linux-x86_64-2.7/Crypto/Protocol
copying lib/Crypto/Protocol/KDF.py -> build/lib.linux-x86_64-2.7/Crypto/Protocol
copying lib/Crypto/Protocol/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Protocol
creating build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/pubkey.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/DSA.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/_RSA.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/ElGamal.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/_slowmath.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/RSA.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
copying lib/Crypto/PublicKey/_DSA.py -> build/lib.linux-x86_64-2.7/Crypto/PublicKey
creating build/lib.linux-x86_64-2.7/Crypto/Signature
copying lib/Crypto/Signature/PKCS1_PSS.py -> build/lib.linux-x86_64-2.7/Crypto/Signature
copying lib/Crypto/Signature/PKCS1_v1_5.py -> build/lib.linux-x86_64-2.7/Crypto/Signature
copying lib/Crypto/Signature/__init__.py -> build/lib.linux-x86_64-2.7/Crypto/Signature
running build_ext
running build_configure
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... configure: error: in `/mnt/cache/scratch/pip-build-9pWjy0/pycrypto':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/mnt/cache/scratch/pip-build-9pWjy0/pycrypto/setup.py", line 456, in <module>
core.setup(**kw)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/opt/cryosparc/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/setuptools/command/install.py", line 61, in run
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/command/install.py", line 563, in run
self.run_command('build')
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/mnt/cache/scratch/pip-build-9pWjy0/pycrypto/setup.py", line 251, in run
self.run_command(cmd_name)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/opt/cryosparc/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/mnt/cache/scratch/pip-build-9pWjy0/pycrypto/setup.py", line 278, in run
raise RuntimeError("autoconf error")
RuntimeError: autoconf error
----------------------------------------
Command "/opt/cryosparc/anaconda2/bin/python -u -c "import setuptools, tokenize;__file__='/mnt/cache/scratch/pip-build-9pWjy0/pycrypto/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /mnt/cache/scratch/pip-VVqtwX-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /mnt/cache/scratch/pip-build-9pWjy0/pycrypto/
Many threads I found on Google suggested it was a dependency problem:
sudo apt-get install build-essential libssl-dev libffi-dev python-dev
However this did not solve the problem in my case. What did the trick was installing cryoSPARC as root (sudo).
Strangely, that was not necessary when I installed it on another Ubuntu machine.