search

gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
11 stars 6 forks source link

libgfortran issue on macOS #55

Closed agitter closed 4 years ago

agitter commented 4 years ago

A user reports

I have not succeeded to run it on local MATLAB installation. I received errors trying to run the SINGE_Example locally (MATLAB R2019b) on a MacBook running macOS 10.15.2. Seems to be an issue with libgfortran, which is required by glmnet.

$ SINGE_Example
…

Invalid MEX-file
'…/SINGE-master/glmnet_matlab/glmnetMex.mexmaci64':
dlopen(…/SINGE-master/glmnet_matlab/glmnetMex.mexmaci64,
6): Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib
Referenced from:
…/SINGE-master/glmnet_matlab/glmnetMex.mexmaci64
Reason: image not found

Error in glmnetControl (line 79)
ivals.pmin, ivals.exmx, ivals.prec, ivals.mxit] =
glmnetMex();

Error in glmnet (line 329)
inparms = glmnetControl();

Error in iLasso_for_SINGE (line 100)
fit = glmnet(Am, bm, params.family, opt);

Error in run_iLasso_row (line 27)
[metric] = iLasso_for_SINGE(m, outs,
lambda,p1,dT,std_dev,params);

Error in SINGE_GLG_Test (line 58)
[for_metric] = run_iLasso_row(m,outs,params,irow);

Error in SINGE (line 20)
SINGE_GLG_Test(Data,'--outdir',outdir,args{:})

Error in SINGE_Example (line 16)
SINGE(data,gene_list,outdir,hyperparameter_file);

I do not have a local machine running macOS, so I cannot reproduce this issue yet. In #54 I started working on testing SINGE with the MATLAB runtime as a workaround.

agitter commented 4 years ago

I was unable to reproduce this issue in MATLAB R2020a running macOS 10.15.5, so I'm going to close this issue. We can reopen it if we get more information.

If anyone runs into this problem, this solution would be a good first step: https://stackoverflow.com/questions/57207357/dyld-library-not-loaded-usr-local-gfortran-lib-libgfortran-3-dylib-reason-im