How to fix pyinstaller missing libraries errors

Question

I'm trying to compile my code to a .exe file using pyinstaller (python 3.7) I get a lot of missing libraries warnings. The python code runs without issue, any ideas why this will not compile or any work arounds?

The libraries exist in my project, they are run in a virtual environment.

I list all the errors I get when running pyinstaller.

382658 WARNING: lib not found: libdcosqb.BFJ36UD5XZWZE5UMOTP5UDYKAJ3LWZ6R.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\fftpack\convolve.cp37-win_amd64.pyd
383033 WARNING: lib not found: libdcosqb.YMN7XEXYADIEZSKAGEVNR4E3MD7AXDG2.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\fftpack\_fftpack.cp37-win_amd64.pyd
384340 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\_fblas.cp37-win_amd64.pyd
384514 WARNING: lib not found: libwrap_dum.7RLH5R2JISEKBCFBO36Q2WZRYRMQ3UWA.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\_fblas.cp37-win_amd64.pyd
384618 WARNING: lib not found: libwrap_dum.SH3SFEZBDNQLZSLNMIU6EDASAOJZWBGV.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\_flapack.cp37-win_amd64.pyd
384670 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\_flapack.cp37-win_amd64.pyd
385038 WARNING: lib not found: libdet.LTYLCBO4PMZORO4V7LBTFOGWP4SICTLE.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\_flinalg.cp37-win_amd64.pyd
385104 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\special\_ellip_harm_2.cp37-win_amd64.pyd
385472 WARNING: lib not found: libspecfun.BHLTWMBI4EYWDACZN4DQUESSDJRJNGEL.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\special\specfun.cp37-win_amd64.pyd
385590 WARNING: lib not found: libdgamln.VA6RUWQPOSOZ3A6HCHGDC5QGV6F47S47.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\special\_ufuncs.cp37-win_amd64.pyd
385655 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\special\_ufuncs.cp37-win_amd64.pyd
386209 WARNING: lib not found: lib_arpack-.POLHCCLHEJG62ZYKW2BBERCOAJAK5RJY.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\sparse\linalg\eigen\arpack\_arpack.cp37-win_amd64.pyd
386389 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\sparse\linalg\dsolve\_superlu.cp37-win_amd64.pyd
386699 WARNING: lib not found: libgetbreak.BS6JTXL5MIEN3QKK6JGNB2DIL4FW34PC.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\sparse\linalg\isolve\_iterative.cp37-win_amd64.pyd
386873 WARNING: lib not found: libblkdta00.7KSOTSAX3JA3FHVFE2DFOBOTBZH2QZP5.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\integrate\lsoda.cp37-win_amd64.pyd
387090 WARNING: lib not found: libdop853.6TJTQZW3I3Q3QIDQHEOBEZKJ3NYRXI4B.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\integrate\_dop.cp37-win_amd64.pyd
387197 WARNING: lib not found: libvode.YFZ273HOYCOOJY4LACRIULVFQ3LK4OU6.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\integrate\vode.cp37-win_amd64.pyd
387362 WARNING: lib not found: libdqag.YFTVUMBBP6AR2HLZOCE5GBIJRU3LBTM3.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\integrate\_quadpack.cp37-win_amd64.pyd
387544 WARNING: lib not found: libblkdta00.7KSOTSAX3JA3FHVFE2DFOBOTBZH2QZP5.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\integrate\_odepack.cp37-win_amd64.pyd
388368 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\spatial\qhull.cp37-win_amd64.pyd
389752 WARNING: lib not found: libnnls.IXEEHJUCGHJL42YZEM6UIEMROJWXHMLJ.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\_nnls.cp37-win_amd64.pyd
389999 WARNING: lib not found: libslsqp_op.SAIY3IIWE5ZUIXQGDHGJTIBQZOJZQGJK.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\_slsqp.cp37-win_amd64.pyd
390361 WARNING: lib not found: libchkder.G7WSOGIYYQO3UWFVEZ3PPXCXR53ADVPA.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\_minpack.cp37-win_amd64.pyd
390479 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\_trlib\_trlib.cp37-win_amd64.pyd
390856 WARNING: lib not found: libcobyla2.25EVUSEBAW7VKISARB7LO3UGZPN2HXE3.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\_cobyla.cp37-win_amd64.pyd
391343 WARNING: lib not found: liblbfgsb.TRL42X2QZ44KYNXUJZZPLQRWALZRDALM.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\_lbfgsb.cp37-win_amd64.pyd
391672 WARNING: lib not found: libdcsrch.I2AOPDCXAPDRFNPWY55H5UE7XZSU5CVN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\optimize\minpack2.cp37-win_amd64.pyd
392036 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\interpolate\_ppoly.cp37-win_amd64.pyd
392721 WARNING: lib not found: libdfitpack.PJU6IBGOYZCWITNVROHYOQAYNGAXO3HT.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\interpolate\dfitpack.cp37-win_amd64.pyd
392839 WARNING: lib not found: libbispeu.5N2XSD7URZS4WTOSLTOG4DDMA4HGB46U.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\interpolate\_fitpack.cp37-win_amd64.pyd
393008 WARNING: lib not found: lib_blas_su.O33AZULTARLEO3UKTTKWIKONGSWQDIGU.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\cython_lapack.cp37-win_amd64.pyd
393060 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\cython_lapack.cp37-win_amd64.pyd
393176 WARNING: lib not found: lib_blas_su.O33AZULTARLEO3UKTTKWIKONGSWQDIGU.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\cython_blas.cp37-win_amd64.pyd
393238 WARNING: lib not found: libopenblas.TXA6YQSD3GCQQC22GEQ54J2UDCXDXHWN.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\linalg\cython_blas.cp37-win_amd64.pyd
405074 WARNING: lib not found: libmvndst.5VXNIPAPINAF5NIHXAFNA4OTHOPNDEWG.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\stats\mvn.cp37-win_amd64.pyd
405237 WARNING: lib not found: libansari.R6EA3HQP5KZ6TAXU4Y4ZVTRPT7UVA53Z.gfortran-win_amd64.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\scipy\stats\statlib.cp37-win_amd64.pyd
407464 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\_proxy_steerable.cp37-win_amd64.pyd
407575 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\_version.cp37-win_amd64.pyd
407684 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\_device.cp37-win_amd64.pyd
407874 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\error.cp37-win_amd64.pyd
407985 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\utils.cp37-win_amd64.pyd
408131 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\context.cp37-win_amd64.pyd
408249 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\_poll.cp37-win_amd64.pyd
408435 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\socket.cp37-win_amd64.pyd
408571 WARNING: lib not found: libzmq.cp37-win_amd64.pyd dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\zmq\backend\cython\message.cp37-win_amd64.pyd
410317 WARNING: lib not found: tbb.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\pptk\processing\estimate_normals\estimate_normals.pyd
410376 WARNING: lib not found: tbbmalloc.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\pptk\processing\estimate_normals\estimate_normals.pyd
410431 WARNING: lib not found: tbb.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\pptk\kdtree\kdtree.pyd
410506 WARNING: lib not found: tbbmalloc.dll dependency of c:\users\gnobles\pointcloudprocessor64\lib\site-packages\pptk\kdtree\kdtree.pyd

Answer 1

Starting SciPy 1.3.2, dlls are not located in an extra-dll subdirectory anymore but inside a .libs one. So, PyInstaller 3.5 SciPy hook will fail.

To make it work properly, put the following in your .spec file:

import os
import scipy

scipy_libs = os.path.join(os.path.dirname(scipy.__file__), '.libs')

a = Analysis(...,
             pathex=[scipy_libs],
             ...

Answer 2

I encountered the same problem and this worked for me!

1. find your scipy dll dependencies at your scipy installation location. mine is:

C:\Users\$UserName\AppData\Local\Programs\Python\Python37\Lib\site-packages\scipy\.libs\

2. create a new folder named 'extra-dll' and copy all the dlls into the folder

C:\Users\$UserName\AppData\Local\Programs\Python\Python37\Lib\site-packages\scipy\extra-dll\

and run pyinstaller again and it works fine!

I found that this problem only happens on Windows 10 and not on Win 7.