Installation problem

[kiter2520]

Hi there,

I'm getting a different error that I haven't seen reported in the other installation problem issues. I'm using python 3.6.1, have tkinter installed, and have a fresh conda environment. The end of the output reads:

```

clang: error: unsupported option '-fopenmp' error: command 'gcc' failed with exit status 1

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

Command "/Users/awilk/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/h8/_vzt21mn4438nr4gg3g_9c_r0000gn/T/pip-install-9h7wa5gi/velocyto/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/h8/_vzt21mn4438nr4gg3g_9c_r0000gn/T/pip-record-3sm16mnz/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/h8/_vzt21mn4438nr4gg3g_9c_r0000gn/T/pip-install-9h7wa5gi/velocyto/ MED-C02TM0GXHTD5:~ awilk$ velocyto --help -bash: velocyto: command not found

Happy to post more output if necessary. 

[linwang6]

Hi, I got the same error,

clang: error: unsupported option '-fopenmp' error: command 'clang' failed with exit status 1

---

Failed building wheel for velocyto

Have you fixed it ? Thanks

Best.

[gioelelm]

It is a compiler error. Try to install compiler provided by conda:

conda install gcc

and/or

conda install llvm

I hope it does the trick

[linwang6]

Thanks!

[gnar5tar]

Had a similar error as well which cleared up after "conda install gcc"

New error pops up tho:

"8:61: fatal error: limits.h: No such file or directory #include_next <limits.h> /*recurse down to the real one */

Anyone had this issue? Thanks!

On Mac OS X Mojave

[rapolaszilionis]

I did have the same problem as gnar5tar. This seems to be related to using macOS Mojave, I found a solution here: https://stackoverflow.com/a/53057706/10641716

Briefly, running: sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /

placed the header limits.h in a location what can be found by the conda version of gcc and solved the problem.

After that the "pip install velocyto" worked fine for me.

[Abigail575]

conda install clang_osx-64 

also worked for me in case anyone else had problems installing gcc with conda