Install scikit-image

Description

I am sorry about this question which is relevant with pip installation that I cannot successfully install it on TX2 after I tried some ways.

My purpose is to import the skimage.

First, I used this commands:

sudo -H python3 -m pip install matplotlib
or 
sudo -H python3 -m pip --no-cache-dir install matplotlib

Then

sudo -H python3 -m pip --no-cache-dir install scikit-image

Reference: https://stackoverflow.com/questions/36056084/raspberry-pi-2-not-able-to-install-scikit-image

install_skimage_error_messages.log (58.9 KB)

Second, I used this commands:

Reference: How to install numpy 、scikit-image、scikit-learn on Jetson TX2?

sudo apt-get update
sudo apt-get install -y build-essential gfortran libatlas-base-dev
sudo pip3 install numpy cython sklearn

Then

sudo -H python3 -m pip install scikit-image

Third, I used this commands:

Reference:

sudo pip3 install Cython
sudo -H pip3 install joblib numpy scipy
sudo -H pip3 install scikit-learn --index-url https://piwheels.org/simple

sudo apt-get install python-dev libfreetype6-dev
sudo apt-get install libfreetype6-dev
sudo ln -s /usr/include/freetype2/freetype/ /usr/include/freetype
sudo apt-get install libfontconfig1-dev
sudo -H pip3 install scikit-image

Then I got the same error that I found I cannot build imagecodecs.

  compilation terminated.
  error: command 'aarch64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for imagecodecs
  Running setup.py clean for imagecodecs
Failed to build imagecodecs
Installing collected packages: imagecodecs, tifffile, pooch, scikit-image
    Running setup.py install for imagecodecs ... error

install_skimage_2.log (26.2 KB)

So far, I always got error on installing imagecodecs.

Environment

JetPack 4.3 version
ubuntu version: 18.04
python3 version: 3.6.9
Tensorflow version: 1.15
TensorRT version: 6.0.1.10
CUDA version: 10.0.326
nvcc: NVIDIA ® Cuda compiler driver Copyright © 2005-2019 NVIDIA Corporation Built on Mon_Mar_11_22:13:24_CDT_2019 Cuda compilation tools, release 10.0, V10.0.326
cuDNN version: 7.6.3

Expect

I can import skimage in python3

May below link can help.

Hi,

Please check this comment for information:

Thanks.

Thanks for your reply!

Unfortunately, I have tried the method from this link (My third test) in my post.
I got the error on installing/ building imagecodecs while I was installing by this command sudo -H pip3 install scikit-image.

Dear @AastaLLL,

Thanks for your Information.

I followed the steps.
However, I got the error at step 3.
I can directly install the scipy by pip but the version is older than installing from source.
so I uninstalled the older version (v1.2.3) and followed the commands at step 3.

The command:

python3 setup.py install --user

I got the error below:

build/src.linux-aarch64-3.6/build/src.linux-aarch64-3.6/scipy/stats/fortranobject.h:189:14: note: previous definition of ‘PyFortran_Type’ was here
 PyTypeObject PyFortran_Type = {
              ^~~~~~~~~~~~~~
In file included from build/src.linux-aarch64-3.6/scipy/stats/statlibmodule.c:16:0:
build/src.linux-aarch64-3.6/build/src.linux-aarch64-3.6/scipy/stats/fortranobject.h:190:0: error: unterminated #if
 #if PY_VERSION_HEX >= 0x03000000
 
build/src.linux-aarch64-3.6/scipy/stats/statlibmodule.c:20:1: error: expected expression before ‘static’
 static PyObject *statlib_error;
 ^~~~~~
error: Command "aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibuild/src.linux-aarch64-3.6/build/src.linux-aarch64-3.6/scipy/stats -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c build/src.linux-aarch64-3.6/build/src.linux-aarch64-3.6/scipy/stats/fortranobject.c -o build/temp.linux-aarch64-3.6/build/src.linux-aarch64-3.6/build/src.linux-aarch64-3.6/scipy/stats/fortranobject.o -MMD -MF build/temp.linux-aarch64-3.6/build/src.linux-aarch64-3.6/build/src.linux-aarch64-3.6/scipy/stats/fortranobject.o.d" failed with exit status 1

Is there any idea about that error?
It is really hard to install on TX2… lol

I don’t mind to re-install something packages or libraries if I can install successfully this scikit-image.

Thank you in advance.

Best regards,
Chieh

Everybody, I can say that I installed all the libs for setup the Scikit-image on Jetson Nano(JP 4.3),
and only shows the errors of installing imagecodes.
I hope Jetson Nano Team can give a solution for this.
Please kindly check.


jet@jet-desktop:/usr/src/cudnn_samples_v7/mnistCUDNN$ sudo pip3 install scikit-image
WARNING: The directory ‘/home/jet/.cache/pip’ or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo’s -H flag.
Collecting scikit-image
Downloading scikit-image-0.17.2.tar.gz (29.8 MB)
|████████████████████████████████| 29.8 MB 1.6 MB/s
Collecting PyWavelets>=1.1.1
Downloading PyWavelets-1.1.1.tar.gz (4.6 MB)
|████████████████████████████████| 4.6 MB 3.5 MB/s
Collecting imageio>=2.3.0
Downloading imageio-2.8.0-py3-none-any.whl (3.3 MB)
|████████████████████████████████| 3.3 MB 4.3 MB/s
Requirement already satisfied: matplotlib!=3.0.0,>=2.0.0 in /usr/lib/python3/dist-packages (from scikit-image) (2.1.1)
Collecting networkx>=2.0
Downloading networkx-2.4-py3-none-any.whl (1.6 MB)
|████████████████████████████████| 1.6 MB 4.2 MB/s
Requirement already satisfied: numpy>=1.15.1 in /usr/local/lib/python3.6/dist-packages (from scikit-image) (1.18.4)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image) (5.1.0)
Requirement already satisfied: scipy>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from scikit-image) (1.4.1)
Collecting tifffile>=2019.7.26
Downloading tifffile-2020.5.11-py3-none-any.whl (132 kB)
|████████████████████████████████| 132 kB 4.0 MB/s
Collecting decorator>=4.3.0
Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting imagecodecs>=2020.2.18
Downloading imagecodecs-2020.2.18.tar.gz (8.8 MB)
|████████████████████████████████| 8.8 MB 2.8 MB/s
Building wheels for collected packages: scikit-image, PyWavelets, imagecodecs
Building wheel for scikit-image (setup.py) … done
Created wheel for scikit-image: filename=scikit_image-0.17.2-cp36-cp36m-linux_aarch64.whl size=24840165 sha256=064fa678a85f4f15ebea9a6525ef2e34cdcd8fce27e599ffcd9debcef60f3b33
Stored in directory: /tmp/pip-ephem-wheel-cache-rh3uiq0v/wheels/95/df/81/38e2d698d8c3605baff734ff6a1fe1c277e920f5fd0bd0b29d
Building wheel for PyWavelets (setup.py) … done
Created wheel for PyWavelets: filename=PyWavelets-1.1.1-cp36-cp36m-linux_aarch64.whl size=5714778 sha256=e033f87ca6d0efe7893493aa39ba8eff7acfdaad05eae97bf005802c95e021c8
Stored in directory: /tmp/pip-ephem-wheel-cache-rh3uiq0v/wheels/77/30/86/528105a88c8ae72ca512f1b1ea8dc4ccaab8ea4b38513e1c52
Building wheel for imagecodecs (setup.py) … error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-install-uf6adwmi/imagecodecs/setup.py’"’"’; file=’"’"’/tmp/pip-install-uf6adwmi/imagecodecs/setup.py’"’"’;f=getattr(tokenize, ‘"’"‘open’"’"’, open)(file);code=f.read().replace(’"’"’\r\n’"’"’, ‘"’"’\n’"’"’);f.close();exec(compile(code, file, ‘"’"‘exec’"’"’))’ bdist_wheel -d /tmp/pip-wheel-8zu2hfts
cwd: /tmp/pip-install-uf6adwmi/imagecodecs/
Complete output (328 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-aarch64-3.6
creating build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/imagecodecs.py -> build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/main.py -> build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/_imagecodecs.py -> build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/init.py -> build/lib.linux-aarch64-3.6/imagecodecs
creating build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libjpeg-turbo -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-lcms2 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-liblzma -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-snappy -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-charls -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-bitshuffle -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-brotli -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-brunsli -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libpng -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-jpg_0xc3 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zopfli -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-jpeg -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-bzip2 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zstd -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libaec -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-blosc -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-jxrlib -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-fastlz -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zfp -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libwebp -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-giflib -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-lz4 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-lzf -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zlib -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libtiff -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libmng -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-openjpeg -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
running build_ext
skipping ‘imagecodecs/_aec.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_bitshuffle.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_blosc.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_brotli.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_bz2.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_gif.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_imcd.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpeg2k.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpeg8.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpegsof3.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpegxr.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_lz4.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_lzf.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_lzma.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_png.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_shared.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_snappy.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_tiff.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_webp.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_zlib.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_zopfli.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_zstd.c’ Cython extension (up-to-date)
building ‘imagecodecs._aec’ extension
creating build/temp.linux-aarch64-3.6
creating build/temp.linux-aarch64-3.6/imagecodecs
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c imagecodecs/_aec.c -o build/temp.linux-aarch64-3.6/imagecodecs/_aec.o
In file included from /usr/include/python3.6m/numpy/ndarraytypes.h:1809:0,
from /usr/include/python3.6m/numpy/ndarrayobject.h:18,
from /usr/include/python3.6m/numpy/arrayobject.h:4,
from imagecodecs/_aec.c:598:
/usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning "Using deprecated NumPy API, disable it by "
^~~~~~~
aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/imagecodecs/_aec.o -lm -laec -o build/lib.linux-aarch64-3.6/imagecodecs/_aec.cpython-36m-aarch64-linux-gnu.so
building ‘imagecodecs._bitshuffle’ extension
creating build/temp.linux-aarch64-3.6/bitshuffle-0.3.5
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -Ibitshuffle-0.3.5 -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c imagecodecs/_bitshuffle.c -o build/temp.linux-aarch64-3.6/imagecodecs/_bitshuffle.o
In file included from /usr/include/python3.6m/numpy/ndarraytypes.h:1809:0,
from /usr/include/python3.6m/numpy/ndarrayobject.h:18,
from /usr/include/python3.6m/numpy/arrayobject.h:4,
from imagecodecs/_bitshuffle.c:598:
/usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning "Using deprecated NumPy API, disable it by "
^~~~~~~
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -Ibitshuffle-0.3.5 -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c bitshuffle-0.3.5/bitshuffle_core.c -o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/bitshuffle_core.o
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_elem_NEON_16’:
bitshuffle-0.3.5/bitshuffle_core.c:391:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + 2ii + 016);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:392:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + 2
ii + 1
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:406:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 0
size + ii, a0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:407:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 1
size + ii, b0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char }’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_elem_NEON_32’:
bitshuffle-0.3.5/bitshuffle_core.c:427:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + 4
ii + 0
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:428:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + 4
ii + 1
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:429:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
c0 = vld1q_s8(in_b + 4
ii + 2
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:430:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
d0 = vld1q_s8(in_b + 4
ii + 3
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_elem_NEON_64’:
bitshuffle-0.3.5/bitshuffle_core.c:473:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + 8
ii + 0
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:474:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + 8
ii + 1
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:475:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
c0 = vld1q_s8(in_b + 8
ii + 2
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:476:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
d0 = vld1q_s8(in_b + 8
ii + 3
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:477:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
e0 = vld1q_s8(in_b + 8
ii + 4
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:478:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
f0 = vld1q_s8(in_b + 8
ii + 5
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:479:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
g0 = vld1q_s8(in_b + 8
ii + 6
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:480:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
h0 = vld1q_s8(in_b + 8
ii + 7
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:518:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 0
size + ii, a0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:519:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 1
size + ii, b0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:520:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 2
size + ii, c0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:521:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 3
size + ii, d0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:522:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 4
size + ii, e0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:523:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 5
size + ii, f0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:524:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 6
size + ii, g0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:525:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 7
size + ii, h0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char *’
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_bitrow_NEON’:
bitshuffle-0.3.5/bitshuffle_core.c:683:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + (ii + 0)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:684:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + (ii + 1)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:685:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
c0 = vld1q_s8(in_b + (ii + 2)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:686:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
d0 = vld1q_s8(in_b + (ii + 3)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:687:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
e0 = vld1q_s8(in_b + (ii + 4)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:688:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
f0 = vld1q_s8(in_b + (ii + 5)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:689:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
g0 = vld1q_s8(in_b + (ii + 6)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:690:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
h0 = vld1q_s8(in_b + (ii + 7)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -Ibitshuffle-0.3.5 -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c bitshuffle-0.3.5/iochain.c -o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/iochain.o
aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/imagecodecs/_bitshuffle.o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/bitshuffle_core.o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/iochain.o -lm -o build/lib.linux-aarch64-3.6/imagecodecs/_bitshuffle.cpython-36m-aarch64-linux-gnu.so
building ‘imagecodecs._blosc’ extension
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c imagecodecs/_blosc.c -o build/temp.linux-aarch64-3.6/imagecodecs/_blosc.o
In file included from /usr/include/python3.6m/numpy/ndarraytypes.h:1809:0,
from /usr/include/python3.6m/numpy/ndarrayobject.h:18,
from /usr/include/python3.6m/numpy/arrayobject.h:4,
from imagecodecs/_blosc.c:598:
/usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning "Using deprecated NumPy API, disable it by "
^~~~~~~
imagecodecs/_blosc.c:602:10: fatal error: blosc.h: No such file or directory
#include “blosc.h”
^~~~~~~~~
compilation terminated.
error: command ‘aarch64-linux-gnu-gcc’ failed with exit status 1

ERROR: Failed building wheel for imagecodecs
Running setup.py clean for imagecodecs
Successfully built scikit-image PyWavelets
Failed to build imagecodecs
Installing collected packages: PyWavelets, imageio, decorator, networkx, imagecodecs, tifffile, scikit-image
Attempting uninstall: decorator
Found existing installation: decorator 4.1.2
Uninstalling decorator-4.1.2:
Successfully uninstalled decorator-4.1.2
Running setup.py install for imagecodecs … error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’"’/tmp/pip-install-uf6adwmi/imagecodecs/setup.py’"’"’; file=’"’"’/tmp/pip-install-uf6adwmi/imagecodecs/setup.py’"’"’;f=getattr(tokenize, ‘"’"‘open’"’"’, open)(file);code=f.read().replace(’"’"’\r\n’"’"’, ‘"’"’\n’"’"’);f.close();exec(compile(code, file, ‘"’"‘exec’"’"’))’ install --record /tmp/pip-record-ioo5rlfp/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/imagecodecs
cwd: /tmp/pip-install-uf6adwmi/imagecodecs/
Complete output (328 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-aarch64-3.6
creating build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/imagecodecs.py -> build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/main.py -> build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/_imagecodecs.py -> build/lib.linux-aarch64-3.6/imagecodecs
copying imagecodecs/init.py -> build/lib.linux-aarch64-3.6/imagecodecs
creating build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libjpeg-turbo -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-lcms2 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-liblzma -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-snappy -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-charls -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-bitshuffle -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-brotli -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-brunsli -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libpng -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-jpg_0xc3 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zopfli -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-jpeg -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-bzip2 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zstd -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libaec -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-blosc -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-jxrlib -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-fastlz -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zfp -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libwebp -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-giflib -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-lz4 -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-lzf -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-zlib -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libtiff -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-libmng -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
copying imagecodecs/licenses/LICENSE-openjpeg -> build/lib.linux-aarch64-3.6/imagecodecs/licenses
running build_ext
skipping ‘imagecodecs/_aec.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_bitshuffle.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_blosc.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_brotli.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_bz2.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_gif.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_imcd.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpeg2k.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpeg8.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpegsof3.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_jpegxr.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_lz4.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_lzf.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_lzma.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_png.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_shared.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_snappy.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_tiff.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_webp.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_zlib.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_zopfli.c’ Cython extension (up-to-date)
skipping ‘imagecodecs/_zstd.c’ Cython extension (up-to-date)
building ‘imagecodecs._aec’ extension
creating build/temp.linux-aarch64-3.6
creating build/temp.linux-aarch64-3.6/imagecodecs
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c imagecodecs/_aec.c -o build/temp.linux-aarch64-3.6/imagecodecs/_aec.o
In file included from /usr/include/python3.6m/numpy/ndarraytypes.h:1809:0,
from /usr/include/python3.6m/numpy/ndarrayobject.h:18,
from /usr/include/python3.6m/numpy/arrayobject.h:4,
from imagecodecs/_aec.c:598:
/usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning “Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning “Using deprecated NumPy API, disable it by "
^~~~~~~
aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/imagecodecs/_aec.o -lm -laec -o build/lib.linux-aarch64-3.6/imagecodecs/_aec.cpython-36m-aarch64-linux-gnu.so
building ‘imagecodecs._bitshuffle’ extension
creating build/temp.linux-aarch64-3.6/bitshuffle-0.3.5
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -Ibitshuffle-0.3.5 -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c imagecodecs/_bitshuffle.c -o build/temp.linux-aarch64-3.6/imagecodecs/_bitshuffle.o
In file included from /usr/include/python3.6m/numpy/ndarraytypes.h:1809:0,
from /usr/include/python3.6m/numpy/ndarrayobject.h:18,
from /usr/include/python3.6m/numpy/arrayobject.h:4,
from imagecodecs/_bitshuffle.c:598:
/usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning “Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning “Using deprecated NumPy API, disable it by "
^~~~~~~
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -Ibitshuffle-0.3.5 -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c bitshuffle-0.3.5/bitshuffle_core.c -o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/bitshuffle_core.o
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_elem_NEON_16’:
bitshuffle-0.3.5/bitshuffle_core.c:391:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + 2ii + 016);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:392:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + 2
ii + 1
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:406:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 0
size + ii, a0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:407:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 1
size + ii, b0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char }’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_elem_NEON_32’:
bitshuffle-0.3.5/bitshuffle_core.c:427:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + 4
ii + 0
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:428:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + 4
ii + 1
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:429:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
c0 = vld1q_s8(in_b + 4
ii + 2
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:430:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
d0 = vld1q_s8(in_b + 4
ii + 3
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_elem_NEON_64’:
bitshuffle-0.3.5/bitshuffle_core.c:473:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + 8
ii + 0
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:474:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + 8
ii + 1
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:475:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
c0 = vld1q_s8(in_b + 8
ii + 2
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:476:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
d0 = vld1q_s8(in_b + 8
ii + 3
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:477:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
e0 = vld1q_s8(in_b + 8
ii + 4
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:478:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
f0 = vld1q_s8(in_b + 8
ii + 5
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:479:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
g0 = vld1q_s8(in_b + 8
ii + 6
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char }’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:480:23: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
h0 = vld1q_s8(in_b + 8
ii + 7
16);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:518:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 0
size + ii, a0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:519:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 1
size + ii, b0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:520:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 2
size + ii, c0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:521:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 3
size + ii, d0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:522:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 4
size + ii, e0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:523:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 5
size + ii, f0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:524:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 6
size + ii, g0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:525:18: warning: pointer targets in passing argument 1 of ‘vst1q_s8’ differ in signedness [-Wpointer-sign]
vst1q_s8(out_b + 7
size + ii, h0);
^~~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:26906:1: note: expected ‘int8_t * {aka signed char *}’ but argument is of type ‘char *’
vst1q_s8 (int8_t *a, int8x16_t b)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c: In function ‘bshuf_trans_byte_bitrow_NEON’:
bitshuffle-0.3.5/bitshuffle_core.c:683:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
a0 = vld1q_s8(in_b + (ii + 0)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:684:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
b0 = vld1q_s8(in_b + (ii + 1)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:685:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
c0 = vld1q_s8(in_b + (ii + 2)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:686:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
d0 = vld1q_s8(in_b + (ii + 3)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:687:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
e0 = vld1q_s8(in_b + (ii + 4)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:688:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
f0 = vld1q_s8(in_b + (ii + 5)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:689:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
g0 = vld1q_s8(in_b + (ii + 6)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
bitshuffle-0.3.5/bitshuffle_core.c:690:27: warning: pointer targets in passing argument 1 of ‘vld1q_s8’ differ in signedness [-Wpointer-sign]
h0 = vld1q_s8(in_b + (ii + 7)*nbyte_row + jj);
^~~~
In file included from bitshuffle-0.3.5/bitshuffle_core.c:37:0:
/usr/lib/gcc/aarch64-linux-gnu/7/include/arm_neon.h:17197:1: note: expected ‘const int8_t * {aka const signed char *}’ but argument is of type ‘const char *’
vld1q_s8 (const int8_t *a)
^~~~~~~~
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -Ibitshuffle-0.3.5 -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c bitshuffle-0.3.5/iochain.c -o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/iochain.o
aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-3.6/imagecodecs/_bitshuffle.o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/bitshuffle_core.o build/temp.linux-aarch64-3.6/bitshuffle-0.3.5/iochain.o -lm -o build/lib.linux-aarch64-3.6/imagecodecs/_bitshuffle.cpython-36m-aarch64-linux-gnu.so
building ‘imagecodecs._blosc’ extension
aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -I/usr/include/python3.6m -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -c imagecodecs/_blosc.c -o build/temp.linux-aarch64-3.6/imagecodecs/_blosc.o
In file included from /usr/include/python3.6m/numpy/ndarraytypes.h:1809:0,
from /usr/include/python3.6m/numpy/ndarrayobject.h:18,
from /usr/include/python3.6m/numpy/arrayobject.h:4,
from imagecodecs/_blosc.c:598:
/usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning “Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning “Using deprecated NumPy API, disable it by "
^~~~~~~
imagecodecs/_blosc.c:602:10: fatal error: blosc.h: No such file or directory
#include “blosc.h”
^~~~~~~~~
compilation terminated.
error: command ‘aarch64-linux-gnu-gcc’ failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '”’”’/tmp/pip-install-uf6adwmi/imagecodecs/setup.py’”’”’; file=’”’”’/tmp/pip-install-uf6adwmi/imagecodecs/setup.py’"’"’;f=getattr(tokenize, ‘"’"‘open’"’"’, open)(file);code=f.read().replace(’"’"’\r\n’"’"’, ‘"’"’\n’"’"’);f.close();exec(compile(code, file, ‘"’"‘exec’"’"’))’ install --record /tmp/pip-record-ioo5rlfp/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/imagecodecs Check the logs for full command output.

Any updates? I’m having the same issue on Nano.

Hi

We tried the whole process, the dependency is a little complex.
You can refer the steps as bellow.
https://forum.miivii.com/forum.php?mod=viewthread&tid=263&page=1&extra=#pid303

imagecodecs== 2020.2.18 Installation

Install Ubuntu18.04 Dependency

sudo apt install cython libaec-dev libblosc-dev libbrotli-dev libghc-bzlib-dev libgif-dev libopenjp2-7-dev liblcms2-dev libjpeg-dev libjxr-dev liblz4-dev liblzma-dev libpng-dev libsnappy-dev libtiff-dev python3-numpy

Adjust header file location(A little disgusting…)

sudo ln -s /usr/include/openjpeg-2.3/* /usr/include/
sudo ln -s /usr/include/jxrlib/* /usr/include/

Install brunsli v0.1,you can’t get through apt

git clone https://github.com/google/brunsli.git
cd brunsli
git checkout v0.1
git submodule update --init --recursive
mkdir build && cd build
cmake … -DCMAKE_BUILD_TYPE=Release
make
sudo make install

**Install libtiff 4.1.0,to replace 4.0.9,or ** error: ‘COMPRESSION_ZSTD’ undeclared happens

sudo apt purge libtiff-dev
git clone https://gitlab.com/libtiff/libtiff
cd libtiff/
git checkout v4.1.0
./autogen.sh
./configure
make
sudo make install

install with pip

pip3 install imagecodecs==2020.2.18 -i https://pypi.tuna.tsinghua.edu.cn/simple

Successfully installed imagecodecs-2020.2.18

Thanks.

1 Like

Hi @apacheindex

I suggest next time you can save your output messages into a .txt file, then uploading an attachment.
Or you should use the ``` this markdown program syntax to show your terminal information.

Thanks.

There is a ton of dependencies needed to imagecodecs, which in turn is a dependency for scikit-image.

I suggest to you double check if all of them are installed. For me, it worked.

sudo apt-get install build-essential python3-dev cython3 python3-setuptools python3-pip python3-wheel python3-numpy python3-pytest python3-blosc python3-brotli python3-snappy python3-lz4 libz-dev libblosc-dev liblzma-dev liblz4-dev libzstd-dev libpng-dev libwebp-dev libbz2-dev libopenjp2-7-dev libjpeg-turbo8-dev libjxr-dev liblcms2-dev libcharls-dev libaec-dev libbrotli-dev libsnappy-dev libzopfli-dev libgif-dev libtiff-dev

Hi,

Sorry that it takes some time to figure out the dependencies.
Here are the detail building steps for scikit-image.

1. Dependencies

$ sudo apt-get install liblapack-dev gfortran
$ sudo apt-get install python3-pip
$ sudo pip3 install -U pip
$ sudo pip3 install Cython numpy

2. Scipy

$ wget https://github.com/scipy/scipy/releases/download/v1.3.3/scipy-1.3.3.tar.gz
$ tar -xzvf scipy-1.3.3.tar.gz scipy-1.3.3
$ cd scipy-1.3.3/
$ python3 setup.py install --user

3. Tiff

$ wget https://download.osgeo.org/libtiff/tiff-4.1.0.tar.gz
$ tar -xzvf tiff-4.1.0.tar.gz
$ cd tiff-4.1.0/
$ ./configure
$ make
$ sudo make install

4. Scikit-image

$ sudo apt-get install python3-sklearn
$ sudo apt-get install libaec-dev libblosc-dev libffi-dev libbrotli-dev libboost-all-dev libbz2-dev
$ sudo apt-get install libgif-dev libopenjp2-7-dev liblcms2-dev libjpeg-dev libjxr-dev liblz4-dev liblzma-dev libpng-dev libsnappy-dev libwebp-dev libzopfli-dev libzstd-dev
$ sudo pip3 install imagecodecs
$ sudo pip3 install scikit-image

5. Test

nvidia@nvidia-desktop:~$ python3
Python 3.6.9 (default, Apr 18 2020, 01:56:04) 
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import skimage
>>> skimage.__version__
'0.17.2'

Thanks.

4 Likes

Dear @AastaLLL,

Thank you so much for your kind favor.
I have tried many different ways, and I all got stuck. But using your way, it works!

Screenshot at 15-22-54

Thanks a lot!

Sincerely,
Chieh

Good to know this!

I tried these steps. However, the installation fails while running the imagecodecs command, citing that “openjpeg.h” is not found. Any way to resolve this?

same here! when i sudo pip3 install imagecodecs i get a very large error output, i dont know why is this happening, but i have similar ussues whit the pip, numpy and h5py libs

Dear guys,

I think if your environment settings are not totally as same as mine, it is better for you to create a new topic.
Of course, you can refer to this post in your topic.

Cheers!