search

velocyto-team / velocyto.R

RNA velocity estimation in R
http://velocyto.org
177 stars 215 forks source link

clang: error: unsupported option '-fopenmp' #99

Open Thralni opened 5 years ago

Thralni commented 5 years ago

Hello,

I realize this issue has been posted over and over again but I can't for the life of me seem to fix it. I tried suggestions in other threads, and I still bump into this same error:

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/benjaminvansoldt/miniconda3/include -arch x86_64 -I/Users/benjaminvansoldt/miniconda3/include -arch x86_64 -I/Users/benjaminvansoldt/miniconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/benjaminvansoldt/miniconda3/include/python3.7m -c velocyto/speedboosted.c -o build/temp.macosx-10.7-x86_64-3.7/velocyto/speedboosted.o -fopenmp -ffast-math clang: error: unsupported option '-fopenmp' error: command 'gcc' failed with exit status 1

I understand this has to do with clang4 on Apple not supporting OpenMP. As was suggeste din other threads, I tried installing different versions of gcc through Conda, but none of that solved the problem either.

This just led to a message saying the package gcc doesn't exist: conda install gcc

llvm was installed it seems but didn't solve the issue: conda install llvm

And finally tried libgcc (as well as compiling from the forge) but that also didn't help: conda install libgcc

So at this point I'm pretty stuck. I'm a total beginner with Python, and so have no idea what else to try. I've got Velocyto working in R, until I realize there are some pre-processing steps that need to be done to the data to create the spliced/unspliced annotations. I intend to do this using the velocyto.py method discussed in the tutorial.

Any help would be immensely appreciated!

CoderMatthias commented 5 years ago

I had the same issue with gcc not existing. I got it to install using:

conda install -c anaconda gcc

Hope this works for you.

Thralni commented 5 years ago

I had actually tried that one as well, but Anaconda can't find the package...

GrigoriiNos commented 5 years ago

Got the similar issue, here is my error

clang: error: unsupported option '-fopenmp' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘velocyto.R’

installing gcc, llvm, libgcc doesn't help

jayden199012 commented 4 years ago

Got the similar issue, here is my error

clang: error: unsupported option '-fopenmp' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘velocyto.R’

  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/velocyto.R’ Error: Failed to install 'velocyto.R' from GitHub: (converted from warning) installation of package ‘/var/folders/6n/fybw2ts966dc3jhc1gqw8hxh90fnjj/T//Rtmp5Ugx7c/file3f5771d8fdc9/velocyto.R_0.6.tar.gz’ had non-zero exit status

installing gcc, llvm, libgcc doesn't help

Did you manage to find a solution? I am facing the same issue now

samIndeed commented 4 years ago

Hi,

I'm having a similar problem. The only channel that seems to almost work is

conda install -c conda-forge gcc

But that doesn't seem to work either. Here is the start of the output

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining conflict for anaconda astroid lazy-object-proxy pylint: : 307it [44:21Examining conflict for anaconda astroid lazy-object-proxy pylint: : 308it [44:21Examining conflict for anaconda astroid pylint: : 308it [44:25, 2.76s/it] Examining conflict for mpmath anaconda gmpy2 sympy scipy gcc mpc: : 309it [44:30Examining conflict for mpmath anaconda gmpy2 sympy scipy gcc mpc: : 310it [44:30Examining conflict for anaconda gmpy2 sympy mpmath: : 310it [44:36, 3.59s/it] Examining conflict for anaconda sphinxcontrib-websupport sphinx sphinxcontrib: :Examining conflict for anaconda sphinxcontrib-websupport sphinx sphinxcontrib: :Examining conflict for anaconda scikit-learn nltk: : 318it [45:00, 3.71s/it] Examining conflict for joblib anaconda scikit-learn nltk: : 319it [45:04, 3.91sExamining conflict for joblib anaconda scikit-learn nltk: : 320it [45:04, 3.99sExamining conflict for patsy anaconda scikit-learn seaborn statsmodels nltk scipExamining conflict for patsy anaconda scikit-learn seaborn statsmodels nltk scipExamining conflict for anaconda _ipyw_jlab_nb_ext_conf jupyterlab: : 321it [45:1Examining conflict for anaconda _ipyw_jlab_nb_ext_conf jupyterlab: : 322it [45:1Examining conflict for _ipyw_jlab_nb_ext_conf jupyterlab: : 322it [45:22, 5.54sExamining conflict for _ipyw_jlab_nb_ext_conf jupyterlab: : 323it [45:22, 5.14sExamining conflict for anaconda jbig: : 323it [45:22, 5.14s/it] Examining conflict for anaconda patsy statsmodels seaborn: : 325it [45:22, 3.67Examining conflict for anaconda statsmodels seaborn: : 326it [45:28, 3.67s/ifailed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

  • anaconda-navigator -> python[version='2.7.|3.5.|3.6.|3.4.']
  • anaconda-project -> python[version='3.4.*|>=3.8,<3.9.0a0']
  • anaconda==2020.02 -> python[version='3.6.10|3.7.6|3.8.1',build='h359304d_0|h359304d_2|h359304d_1']
  • autopep8 -> python[version='>=3.8,<3.9.0a0']
  • backports.functools_lru_cache -> python[version='2.7.|3.5.|3.6.|3.4.|>=2.7,<2.8.0a0']
  • bkcharts -> python=3.4
PrashINRA commented 4 years ago

The same problem, I am having! I tried to git clone the library on my Mac and then - devtools::install_local("velocyto.R-master")

But still having the same error- clang: error: unsupported option '-fopenmp' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘velocyto.R’

Any ideas now?

samIndeed commented 4 years ago

Hi Prash, I'm not sure but it might be worth trying scvelo instead. That's what I'm using now.

Thralni commented 4 years ago

Just to circle back... I never was able to get this to run. I eventually gave up and asked my bioinformatics collaborator to do it for me...

evanbiederstedt commented 4 years ago

There's a solution provided here: https://github.com/kharchenkolab/conos/wiki/Installing-Conos-for-Mac-OS