Raspberry PI : error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1

[leonardoee]

Hi,
I've been facing the a similar issue from [https://github.com//issues/414#issue-532885738]
when installing PyMuPDF on my raspberry Pi. I've been trying work this out for more than a week. Just to highlight, I'm a beginner on coding and linux.

Firstly when I ran "pip install PyMuPDF" I got the error bellow:
"command 'arm-linux-gnueabihf-gcc' failed with exit status 1"
The same error happened with I downloaded and tried to install PyMuPDF-master by "python setup.py install"

After several unsuccessful tries and errors installing all sorts of packages when I ran "python setup.py install" from PyMuPDF-master I got a slightly different error:
"error: command 'gcc' failed with exit status 1"

I did all the steps on the links bellow, but nothing worked.
https://solarianprogrammer.com/2018/05/06/building-gcc-cross-compiler-raspberry-pi/
https://github.com/Pro/raspi-toolchain

Appreciate any help on this.

[JorjMcKie]

There are fundamental differences in the install methods you used. When installing PyMuPDF you have two options:

1. install from a (pre-compiled) "wheel"
2. install from sources

Ad 1.

Wheel refers to the extensions .whl of the single installation file required. It is a ZIP format. It can contained any mixture of Python files, binary pre-compiled Python extensions and potentially arbitrary other files.
The installation steps for wheels require no compiler and basically are just file copies to the respective Python dist-packages or site-packages folder.
I am preparing such wheels for PyMuPDF. Every combination of target operating system, Python version and bitness needs its own specific wheel file. There are currently 16 wheel files: Linux and OSX 4 each for the Python 64bit versions 3.6, 3.7, 3.8, 3.9, and 8 for Windows - same Python versions, but each with 32bit and 64bit.
If you execute python -m pip install pymupdf on any platform, PIP will determine the platform on which it has been invoked, generate a file name from this information and download the matching wheel from PyPI. If that file is not on PyPI, then pip will download the PyMuPDF source installation material from PyPI and execute python setup.py install with it. This is equivalent to alternative 2 following.

Ad 2.

You can generate PyMuPDF from sources. This obviously requires a C compiler suitable for the desired target platform. In addition, you must download and generate MuPDF (Artifex Software Inc.) before generating PyMuPDF.

Obviously, a lot can go wrong with this approach.

You did not specify any details of the encountered errors. So there is no way to tell what really happened. But they all indicate, that the "source generation" alternative has been tried to execute.
And of course that was bound to fail, if no previous MuPDF installation existed.

So what may be next steps:

• Either install build MuPDF. This must happen with a C compiler suitable for the intended target environment. Maybe other adjustments to the MuPDF build process are required, too.
• Or, build a wheel that can work with your RPI. If this can be done, you are out of trouble.

I am currently developping additional wheels for ARM environments. Maybe there is a chance to make one for you.
What is the bitness of this RPI environment: 32bit / 64bit and the Python version?

[leonardoee]

Hi,
Firstly, thank you for this quick turnaround.
This library is great. I was amazed when I saw my script ran in 1/3 of the time compared to when I was using PyPDF2 + reportlab.
I'm running Raspbian GNU/Linux 10 (buster) - 32bits, kernel: Linux raspberrypi 5.10.17-v7l+ #1403 armv7l GNU/Linux and python 3.7.3.
I have no issues on changing the python version to match an existent wheel.
Bellow is the error I've been facing when I run python -m pip install pymupdf

pi@raspberrypi:~/dev/guidegf/sggen $ python3 -m pip install pymupdf
Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
Collecting pymupdf
Using cached PyMuPDF-1.18.9.tar.gz (308 kB)
Building wheels for collected packages: pymupdf
Building wheel for pymupdf (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/pi/dev/guidegf/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/setup.py'"'"'; file='"'"'/tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/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-4ualunyb
cwd: /tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/
Complete output (20 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-armv7l-3.7
creating build/lib.linux-armv7l-3.7/fitz
copying fitz/init.py -> build/lib.linux-armv7l-3.7/fitz
copying fitz/fitz.py -> build/lib.linux-armv7l-3.7/fitz
copying fitz/utils.py -> build/lib.linux-armv7l-3.7/fitz
copying fitz/main.py -> build/lib.linux-armv7l-3.7/fitz
running build_ext
building 'fitz._fitz' extension
creating build/temp.linux-armv7l-3.7
creating build/temp.linux-armv7l-3.7/fitz
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/mupdf -I/usr/local/include/mupdf -Imupdf/thirdparty/freetype/include -I/home/pi/dev/guidegf/include -I/usr/include/python3.7m -c fitz/fitz_wrap.c -o build/temp.linux-armv7l-3.7/fitz/fitz_wrap.o
fitz/fitz_wrap.c:2767:10: fatal error: fitz.h: No such file or directory
#include <fitz.h>
^~~~~~~~
compilation terminated.
error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1

ERROR: Failed building wheel for pymupdf
Running setup.py clean for pymupdf
Failed to build pymupdf
Installing collected packages: pymupdf
Running setup.py install for pymupdf ... error
ERROR: Command errored out with exit status 1:
command: /home/pi/dev/guidegf/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/setup.py'"'"'; file='"'"'/tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/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-wgla2cn2/install-record.txt --single-version-externally-managed --compile --install-headers /home/pi/dev/guidegf/include/site/python3.7/pymupdf
cwd: /tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/
Complete output (20 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-armv7l-3.7
creating build/lib.linux-armv7l-3.7/fitz
copying fitz/init.py -> build/lib.linux-armv7l-3.7/fitz
copying fitz/fitz.py -> build/lib.linux-armv7l-3.7/fitz
copying fitz/utils.py -> build/lib.linux-armv7l-3.7/fitz
copying fitz/main.py -> build/lib.linux-armv7l-3.7/fitz
running build_ext
building 'fitz._fitz' extension
creating build/temp.linux-armv7l-3.7
creating build/temp.linux-armv7l-3.7/fitz
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/mupdf -I/usr/local/include/mupdf -Imupdf/thirdparty/freetype/include -I/home/pi/dev/guidegf/include -I/usr/include/python3.7m -c fitz/fitz_wrap.c -o build/temp.linux-armv7l-3.7/fitz/fitz_wrap.o
fitz/fitz_wrap.c:2767:10: fatal error: fitz.h: No such file or directory
#include <fitz.h>
^~~~~~~~
compilation terminated.
error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/pi/dev/guidegf/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/setup.py'"'"'; file='"'"'/tmp/pip-install-uxmi137a/pymupdf_8e4bd29fef5b46e9be53199a6ba101da/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-wgla2cn2/install-record.txt --single-version-externally-managed --compile --install-headers /home/pi/dev/guidegf/include/site/python3.7/pymupdf Check the logs for full command output.

Really appreciate the help.

[JorjMcKie]

These errors indicate, that MuPDF has not been previously installed.
Either this - or the PyMuPDF setup.py has not been adjusted to point to the correct MuPDF installation libraries.

[leonardoee]

Hi Jorj,

I'm having trouble to install MuPDF. Below is the error I have when I run make prefix=/usr/local install:

pi@pi:/gcc_all/mupdf $ make prefix=/usr/local install
CC build/debug/pdf/pdf-pkcs7.o
source/pdf/pdf-pkcs7.c: In function ‘bsegs_read’:
source/pdf/pdf-pkcs7.c:30:39: error: dereferencing pointer to incomplete type ‘BIO’ {aka ‘struct bio_st’}
BIO_SEGS_CTX *ctx = (BIO_SEGS_CTX *)b->ptr;
^~
source/pdf/pdf-pkcs7.c: At top level:
source/pdf/pdf-pkcs7.c:107:1: error: variable ‘methods_bsegs’ has initializer but incomplete type
static BIO_METHOD methods_bsegs =
^~~~~~
source/pdf/pdf-pkcs7.c:109:2: warning: excess elements in struct initializer
0,"segment reader",
^
source/pdf/pdf-pkcs7.c:109:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:109:4: warning: excess elements in struct initializer
0,"segment reader",
^~~~~~~~~~~~~~~~
source/pdf/pdf-pkcs7.c:109:4: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:110:2: warning: excess elements in struct initializer
NULL,
^~~~
source/pdf/pdf-pkcs7.c:110:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:111:2: warning: excess elements in struct initializer
bsegs_read,
^~~~~~~~~~
source/pdf/pdf-pkcs7.c:111:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:112:2: warning: excess elements in struct initializer
NULL,
^~~~
source/pdf/pdf-pkcs7.c:112:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:113:2: warning: excess elements in struct initializer
NULL,
^~~~
source/pdf/pdf-pkcs7.c:113:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:114:2: warning: excess elements in struct initializer
bsegs_ctrl,
^~~~~~~~~~
source/pdf/pdf-pkcs7.c:114:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:115:2: warning: excess elements in struct initializer
bsegs_new,
^~~~~~~~~
source/pdf/pdf-pkcs7.c:115:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:116:2: warning: excess elements in struct initializer
bsegs_free,
^~~~~~~~~~
source/pdf/pdf-pkcs7.c:116:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:117:2: warning: excess elements in struct initializer
bsegs_callback_ctrl,
^~~~~~~~~~~~~~~~~~~
source/pdf/pdf-pkcs7.c:117:2: note: (near initialization for ‘methods_bsegs’)
source/pdf/pdf-pkcs7.c:135:17: error: field ‘x509_ctx’ has incomplete type
X509_STORE_CTX x509_ctx;
^~~~~~~~
source/pdf/pdf-pkcs7.c: In function ‘verify_callback’:
source/pdf/pdf-pkcs7.c:159:13: error: dereferencing pointer to incomplete type ‘X509_STORE_CTX’ {aka ‘struct x509_store_ctx_st’}
switch (ctx->error)
^~
source/pdf/pdf-pkcs7.c: In function ‘pk7_verify’:
source/pdf/pdf-pkcs7.c:208:40: error: dereferencing pointer to incomplete type ‘X509_STORE’ {aka ‘struct x509_store_st’}
X509_VERIFY_PARAM_set_flags(cert_store->param, X509_V_FLAG_CB_ISSUER_CHECK);
^~
source/pdf/pdf-pkcs7.c: At top level:
source/pdf/pdf-pkcs7.c:107:19: error: storage size of ‘methods_bsegs’ isn’t known
static BIO_METHOD methods_bsegs =
^~~~~~~~~~~~~
source/pdf/pdf-pkcs7.c: In function ‘bsegs_ctrl’:
source/pdf/pdf-pkcs7.c:66:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
source/pdf/pdf-pkcs7.c: In function ‘bsegs_callback_ctrl’:
source/pdf/pdf-pkcs7.c:105:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
make: [Makefile:136: build/debug/pdf/pdf-pkcs7.o] Error 1

Would installing 64bits Raspian solve these issues?

[viertel97]

@JorjMcKie Thank you!
I can confirm, that files are there, but with every "pip3 install *_aarch64.whl" (with or without sudo) file i receive the error "[filename] is not a supported wheel on this platform". The aarch64 packes should be right, shouldnt they?

[JorjMcKie]

1. I would never just execute pip3, but instead always use the correct Python and then do python -m pip ....
2. You must make sure that you have the current pip. So best always execute python -m pip install -U pip first.
3. Have you confirmed that the aarch64 wheel is there with that same Python version?

[viertel97]

I did all the steps you mentioned. The newest version is installed and i used the cp37 wheel which is for the python 3.7 version, am i correct?
If i try it, this is the output:

pi@raspberrypi:~ $ uname -a
Linux raspberrypi 5.10.17-v8+ #1403 SMP PREEMPT Mon Feb 22 11:37:54 GMT 2021 aarch64 GNU/Linux

pi@raspberrypi:~ $ python3 -m pip --version
pip 22.0.3 from /home/pi/.local/lib/python3.7/site-packages/pip (python 3.7)

pi@raspberrypi:~ $ python3 -m pip install PyMuPDF-1.19.5-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Defaulting to user installation because normal site-packages is not writeable
Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
ERROR: PyMuPDF-1.19.5-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl is not a supported wheel on this platform.

A sudo before the python3 removes the Defaulting to user installation because normal site-packages is not writeable.

[JorjMcKie]

Hm, indeed - everything looks as it should. Out of ideas.
Last resort: build from sources. Try to follow the instructions in the installation folder for Linux / Ubuntu, if you want to do that.

[viertel97]

That worked for me! It showed some errors, but after that i could install PyMuPDF via python3 -m pip install PyMuPDF.
Thank you very much for your support!

[topshed]

Thank you. Would it be possible to include 32bit versions for Raspberry Pi OS?

[JorjMcKie]

Would it be possible to include 32bit versions for Raspberry Pi OS?

No, I am afraid. Does not seem to be supported by cibuildwheel.
I recommend you generate from sources locally.