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How to diagnose conan install issue

I have some installation issues with conan
After my Ubuntu 18.04 told "Command 'conan' not found", I guessed the Python
version is wrong. So I attempted to upgrade with the result
$ sudo apt-get install python
python is already the newest version (2.7.15~rc1-1)
However
$ locate python
/var/lib/binfmts/python2.7
/var/lib/binfmts/python3.6
When in this state I attempted to install conan
$ pip install conan
Collecting conan
...
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 PyJWT-1.7.1 PyYAML-5.1.2 astroid-1.6.6 attrs-19.1.0 backports.functools-lru-cache-1.5 bottle-0.12.17 certifi-2019.6.16 chardet-3.0.4 colorama-0.4.1 conan-1.18.0 configparser-3.7.4 deprecation-2.0.6 distro-1.1.0 enum34-1.1.6 fasteners-0.15 future-0.16.0 futures-3.3.0 idna-2.8 isort-4.3.21 lazy-object-proxy-1.4.1 mccabe-0.6.1 monotonic-1.5 node-semver-0.6.1 packaging-19.1 patch-1.16 pluginbase-0.7 pygments-2.4.2 pylint-1.9.5 pyparsing-2.4.2 python-dateutil-2.8.0 requests-2.22.0 singledispatch-3.4.0.3 six-1.12.0 tqdm-4.32.2 urllib3-1.25.3 wrapt-1.11.2
then 'conan' is listed as being installed but
$ conan
Command 'conan' not found, did you mean:
I.e, no error message or warning, just does not install.
I could find out that the path was not listed in my PATH, so I added '~.local/bin'. Now the story goes on with the error message
CMake Error at CMakeLists.txt:90 (include):
include could not find load file:
Conan
I found
https://docs.conan.io/en/latest/howtos/cmake_launch.html.
OK, I inserted in my CMakeLists.txt file line
# Download automatically, you can also just copy the conan.cmake file
if(NOT EXISTS "${CMAKE_BINARY_DIR}/conan.cmake")
message(STATUS "Downloading conan.cmake from https://github.com/conan-io/cmake-conan")
file(DOWNLOAD "https://raw.githubusercontent.com/conan-io/cmake-conan/master/conan.cmake"
"${CMAKE_BINARY_DIR}/conan.cmake")
endif()
include(${CMAKE_BINARY_DIR}/conan.cmake)
conan_cmake_run(REQUIRES Catch2/2.6.0#catchorg/stable
BASIC_SETUP)
I was also advised,
Please specify in command line CMAKE_BUILD_TYPE
(-DCMAKE_BUILD_TYPE=Release)
So I use
cmake .. -DCMAKE_BUILD_TYPE=Release
rather than
cmake ..
Still, I receive
ERROR: compiler not defined for compiler.libcxx
Please define compiler value first too
FATAL_ERROR;conan install command failed.
STATUS;Conan: Compiler GCC>=5, checking major version 7
STATUS;Conan: Checking correct version: 7
About two weeks ago I could install on another system the same project flawlessly. Can I go back somehow to that state? I expected conan to be stable, rather than alpha.
Edit 2:
I issued
conan profile new default --detect --force
The reply is
Found gcc 7
gcc>=5, using the major as version
************************* WARNING: GCC OLD ABI COMPATIBILITY ***********************
Conan detected a GCC version > 5 but has adjusted the 'compiler.libcxx' setting to
'libstdc++' for backwards compatibility.
Your compiler is likely using the new CXX11 ABI by default (libstdc++11).
(I do not really know why in the case of a new project I need backward compatibility) After that,
cmake ..
finally seems to work. I am afraid I will have further issues due to the compiler standards. For example, SystemC defaults to '98, but some other library uses feature needing '14, and now conan forces to use '11. Is there a way to handle all this centrally, specific to MY system?
Concerning the two python versions: I did not install this manually, only some other install programs did so. I do not really know why and which install script causes such doubling. BTW: Ubuntu said that V2.7 is the newest version, although V3.x is also present. I am a bit confused about these version numbers.
I simply made a new install, and did not especially very WHEN the second version of python appeared. I personally do not even use python, only some install scripts could install it.
Whether my system is specific: I do not think so. I just installed Ubuntu 18.04.2, and my primary goal was to install this SystemC related stuff. I really installed ONLY what was declared as missing. (plus livetex, git, etc.)
In the meantime 'cmake ..' terminated. Appearently, the installation by conan terminated OK. However, when configuring my project, gives messages like
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
SCV_INCLUDE_DIRS
The missing files are installed also by conan, using
[requires]
SystemC/2.3.3#minres/stable
SystemCVerification/2.0.1#minres/stable
doxygen_installer/1.8.15#bincrafters/stable
qt/5.12.0#bincrafters/stable
gtest/1.8.1#bincrafters/stable
flex/2.6.4#bincrafters/stable
I am using literally the same files (either my old disk connected to the bus or the new one, using the same cable). The installation made about a month ago runs fine, the new one behaves as described.
It looks like installing and using conan is too complicated for me. I wanted to simplify installation rather than complicate it.

There is a bunch of cases related to installation listed here:
https://docs.conan.io/en/latest/installation.html#known-installation-issues-with-pip
I would say Conan is installed but is not listed in your PATH. You could find Conan in your Python package folder and update your PATH with conan path:
python -m site # list your package folder
find <package folder> -name conan
echo PATH=${PATH}:<package folder> >> ~/.bashrc
source ~/.bashrc

Building Python 3 on OS X: [Python/importlib.h] Error 133

I am trying to build Python (3.5.2) on OS X El Capitan (10.11.5). However, I run into an error when I try to make it. The error seems to be related to _freeze_importlib.
/usr/local/src/Python-3.5.2 $ make
if test "no" != "yes"; then \
./Programs/_freeze_importlib \
./Lib/importlib/_bootstrap.py Python/importlib.h; \
fi
dyld: lazy symbol binding failed: Symbol not found: _getentropy
Referenced from: /usr/local/src/Python-3.5.2/./Programs/_freeze_importlib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _getentropy
Referenced from: /usr/local/src/Python-3.5.2/./Programs/_freeze_importlib
Expected in: /usr/lib/libSystem.B.dylib
/bin/sh: line 1: 56666 Trace/BPT trap: 5 ./Programs/_freeze_importlib ./Lib/importlib/_bootstrap.py Python/importlib.h
make: *** [Python/importlib.h] Error 133
/usr/local/src/Python-3.5.2 $
You can see my steps on GitHub.
The full Terminal output up to the make fail is in a Gist.
I fully acknowledge that this is an academic exercise, as El Capitan comes with Python 2.7.10 and you can easily install Python 3.5.2 with the official OS X installer package or via Homebrew.
The documentation for Using Python on Unix platforms provides build instructions. The documentation for Using Python on a Macintosh specifically says to use the the OS X installer package.
However, it should be possible to build on Mac.
Python on a Macintosh running Mac OS X is in principle very similar to Python on any other Unix platform, but there are a number of additional features such as the IDE and the Package Manager that are worth pointing out.
At this point, I'm not worried about those additional features. Just curious about why I am getting a make error.

Fixed.
In the output of ./configure, I noticed a reference to /Applications/Xcode-beta.app/Contents/Developer/. I installed Xcode 8 (beta) a few days ago. After switching back to the regular Command Line Tools (with Xcode 7.3.1)
sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
make succeeded. Not perfectly.
Python build finished successfully!
The necessary bits to build these optional modules were not found:
_dbm _gdbm _sqlite3
_ssl nis ossaudiodev
spwd zlib
To find the necessary bits, look in setup.py in detect_modules() for the module's name.
Failed to build these modules:
_lzma _tkinter
I hope I don't need those modules.
I've put the full output of ./configure and make in this Gist. I didn't include the output for make install as it was too long and seemed to only repeat the warnings and errors of make.
Notes
I didn't use --enable-framework or --enable-universalsdk.

I think a better solution is xcode-select --install.
If you update Xcode to 8(beta), you have to run xcode-select --install again to install all the build tools with it.
I ran into the same issue as yours and I can successfully install python through brew with Xcode8 after running xcode-select --install.
I hope it would help others with the same issue here.

How do I install python on a windows machine using a cygwin terminal?

I am trying to install python through cygwin on a windows machine in order to make use of a statistical program that can only be implemented using python in a linux environment.
I have run setup-x86_64.exe and installed all python related cygwin packages in an attempt to install python, but when I open a terminal and type python I just get
$ python
-bash: python: command not found
which is the same for all python commands I try so clearly the installation has not occurred. However, I have found a path to Python-2.7.9 which appears to contain the files required to build python from source.
When I run ./configure it is successful, but when I then input make it fails due to:
File "build/temp.cygwin-1.7.35-x86_64-2.7/libffi/fficonfig.py", line 33, in <module>
ffi_sources += ffi_platforms['X86_WIN64']
KeyError: 'X86_WIN64'
Makefile:488: recipe for target 'sharedmods' failed
make: *** [sharedmods] Error 1
Anyone know why make won't work?
The options in ./configure --help are unfamiliar to me, could any of these options allow for successful installation?
Any ideas would be greatly appreciated, thank you.

Cygwin comes with an installer, called setup.exe or setup-x86_64.exe. Just run it and type python to the search box. Then let it install it for you.
python language interpreter is the basic package you need.

So, this question is 3 years old, but this error still happens with most recent versions of Python 2 (tested with 2.7.13 and 2.7.15)
I was able to get python to build by modifying the following file in the build directory.
--- build/temp.cygwin-2.11.1-x86_64-2.7/libffi/fficonfig.py~ 2018-11-03 14:51:53.290000000 -0400
+++ build/temp.cygwin-2.11.1-x86_64-2.7/libffi/fficonfig.py 2018-11-03 14:53:41.793000000 -0400
## -9,6 +9,7 ##
'X86': ['src/x86/ffi.c', 'src/x86/sysv.S', 'src/x86/win32.S'],
'X86_FREEBSD': ['src/x86/ffi.c', 'src/x86/freebsd.S'],
'X86_WIN32': ['src/x86/ffi.c', 'src/x86/win32.S'],
+ 'X86_WIN64': ['src/x86/ffi.c', 'src/x86/win64.S'],
'SPARC': ['src/sparc/ffi.c', 'src/sparc/v8.S', 'src/sparc/v9.S'],
'ALPHA': ['src/alpha/ffi.c', 'src/alpha/osf.S'],
'IA64': ['src/ia64/ffi.c', 'src/ia64/unix.S'],
The source files, in particular src/x86/win64.S, are present in the source tree. For some reason, ./configure does not seem to be properly adding the option to the dictionary in the fficonfig.py file, which causes the KeyError posted in the question. After making this modification, make and make install completed successfully and I was able to install an alternate version of python in addition to the normal Cygwin package.
I'm not yet sure why this happens, but I thought I would attempt to provide a solution to the question actually asked rather than just telling the asker to install a pre-compiled version using the package manager.

Since building Python from source was said to be a bad idea, I assumed my Cygwin was broken. I attempted to uninstall Cygwin following the instructions on the Cygwin website, but I was unable to remove it due to permission difficulties (I use a university-supplied Windows machine). My last resort was to run the Cygwin installation wizard setup-x86_64.exe and uninstall all packages, then run the wizard once more and select the necessary packages again as if starting from new. Miraculously, installing the required packages from scratch solved the problem and I am now running Python through my Cygwin terminal with no errors.

If you want to run Python on Cygwin, you might need to build it from source.
download the source
unpack it to the directory you could delete later, eg: build
run Cygwin, type: cd /path/to/build
run ./configure --help and read the help about the options you'll need
./configure #options
make

biopython test_Tutorial ... FAIL

I'm fairly new to programming. I'm trying to install biopython on mac os x 10.5.
This is what I did so far. 1. installed xcode 2. installed numpy 3. ran these commands in terminal python setup.py build python setup.py test
test reported back one fail.
test_Tutorial ... FAIL
ERROR: Run tutorial doctests.
Traceback (most recent call last): File "test_Tutorial.py", line 152, in test_doctests ValueError: 4 Tutorial doctests failed: test_from_line_05671, test_from_line_06030, test_from_line_06190, test_from_line_06479
Thanks for any help or advice.

That file test_Tutorial.py runs marked examples in the source for the main Biopython Tutorial and Cookbook ( http://biopython.org/DIST/docs/tutorial/Tutorial.html / http://biopython.org/DIST/docs/tutorial/Tutorial.pdf ) to check the examples work as expected. Internally this uses the same library as Python's doctest examples.
The fact that test_Tutorial.py failed is probably a harmless issue with a couple of examples.
Which version of Biopython are you using? If this was an official release that failure is unexpected. If it was a snapshot from the git repository then that is unfortunate. If you are curious, you could try this to see more information:
$ cd Tests
$ python test_Tutorial.py
This kind of issue might be more easily discussed on the Biopython mailing list http://biopython.org/wiki/Mailing_lists

I've found that the easiest way to set up a good programming environment is to use MacPorts, as it has a great way of ensuring that all dependencies are satisfied when installing things. You'll need to be familiar with Terminal and the command line, though.
Install MacPorts for OSX 10.5. Read the documentation too.
Restart.
Open Terminal.app and enter sudo port selfupdate to make sure the portfile definitions are up to date.
Run sudo port install py27-biopython to install the latest version of Python 2 (2.7.3), numpy, and biopython. This will take a while.
Run echo $PATH and make sure that /opt/local/bin and /opt/local/sbin` are at the beginning. They should be.
Run which python and ensure it returns /opt/local/bin/python. If it doesn't, run sudo port install python_select and follow its instructions to select your default python version.
Hopefully, at this point you can run python to enter the interactive interpreter, and import Bio won't give any errors.
Good luck!

Error installing upgrade from Sphinx 1.1 to 1.1.3 for Python 3.2.3 on Windows XP

Following the directions on the Sphinx home page, I opened a command window and entered:
C:\>easy_install -U Sphinx
(I assume the -U option for upgrade should remove the existing version.)
I get the following error messages (I have admin privileges):
Creating c:\python32\lib\site-packages\site.py
Processing Sphinx
Running setup.py -q bdist_egg --dist-dir C:\Sphinx\egg-dist-tmp-tmopj5
error: Setup script exited with error: SandboxViolation:
open('C:\\Python32\\lib\\lib2to3\\Grammar3.2.3.final.0.pickle', 'wb') {}
The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.
This package cannot be safely installed by EasyInstall, and may not
support alternate installation locations even if you run its setup
script by hand. Please inform the package's author and the EasyInstall
maintainers to find out if a fix or workaround is available.
Can anyone help me to understand and fix the problem? Please don't tell me to use pip, I get the same error when I try to install pip with:
C:\>easy_install pip
Thanks in advance for your help.

I encountered this error message while trying to install the requests library. It seems to be related to files that are not generated during the build (http://bugs.python.org/issue15822) but are required if the 2to3 utility is to be used.
A quick fix for me was to build the required pickled grammars manually:
C:\Python33\Lib>..\python.exe -m lib2to3.pgen2.driver lib2to3\Grammar.txt
Generating grammar tables from lib2to3\Grammar.txt
Writing grammar tables to lib2to3\Grammar3.3.1.final.0.pickle
C:\Python33\Lib>..\python.exe -m lib2to3.pgen2.driver lib2to3\PatternGrammar.txt
Generating grammar tables from lib2to3\PatternGrammar.txt
Writing grammar tables to lib2to3\PatternGrammar3.3.1.final.0.pickle
I tested this on python 3.3.1 but I believe the same procedure should work for you.