Failing to install GDAL on python:3.9 as of Nov 8th - Docker

JamieSgro
November 9, 2022
113 views
0 votes
2 Answers

I have a docker container that has been successfully installing GDAL 3.5.0 up until Nov 8th, 2022. The last passing build with the exact same code was on Nov 7th. The failures occur in a remote environment on the default GitHub Action (or AWS codebuild runner), and I haven’t had the same error locally. Without changing the build fails with the below stack trace.

My question is whether anyone can point me in the right direction on where I should focus my investigation based on the output of the stack trace.

The line that fails:

pip3 install --no-cache-dir GDAL==3.5.0

I’ve already ran:

RUN apt-get update && 
    apt-get install -y 
    python3-pip 
    locales 
    libspatialindex-dev 
    gcc 
    && apt-get -t testing install -y --no-install-recommends libgdal-dev 
    && ln -s /usr/lib/ogdi/libvrf.so /usr/lib 
    && rm -rf /var/lib/apt/lists/* 

ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
ENV C_INCLUDE_PATH=/usr/include/gdal

This is the (lengthy) stack trace of the failure:

#11 [dependencies 3/4] RUN pip3 install --no-cache-dir GDAL==3.5.0
#11 sha256:6dbd22edad17147be79b0611f8e1a8f0fdc44a139c8e2e11d393e563d28fbd64
#11 0.757 Collecting GDAL==3.5.0
#11 0.782   Downloading GDAL-3.5.0.tar.gz (752 kB)
#11 0.796      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 752.0/752.0 KB 64.9 MB/s eta 
...
#11 15.20       creating build/temp.linux-x86_64-3.9/extensions
#11 15.20       gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I../../ogr/ogrsf_frmts -I../../gnm -I../../apps -I/usr/local/include/python3.9 -I. -I/usr/include -c extensions/ogr_wrap.cpp -o build/temp.linux-x86_64-3.9/extensions/ogr_wrap.o -I/usr/include/gdal
#11 15.20       creating build/temp.linux-x86_64-3.9/extensions
#11 15.20       building 'osgeo._gnm' extension
#11 15.20       gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I../../ogr/ogrsf_frmts -I../../gnm -I../../apps -I/usr/local/include/python3.9 -I. -I/usr/include -c extensions/gdal_wrap.cpp -o build/temp.linux-x86_64-3.9/extensions/gdal_wrap.o -I/usr/include/gdal
#11 15.20       gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I../../ogr/ogrsf_frmts -I../../gnm -I../../apps -I/usr/local/include/python3.9 -I. -I/usr/include -c extensions/osr_wrap.cpp -o build/temp.linux-x86_64-3.9/extensions/osr_wrap.o -I/usr/include/gdal
#11 15.20       gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I../../ogr/ogrsf_frmts -I../../gnm -I../../apps -I/usr/local/include/python3.9 -I. -I/usr/include -c extensions/gdalconst_wrap.c -o build/temp.linux-x86_64-3.9/extensions/gdalconst_wrap.o -I/usr/include/gdal
#11 15.20       gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I../../ogr/ogrsf_frmts -I../../gnm -I../../apps -I/usr/local/include/python3.9 -I. -I/usr/include -c extensions/gnm_wrap.cpp -o build/temp.linux-x86_64-3.9/extensions/gnm_wrap.o -I/usr/include/gdal
#11 15.20       extensions/gdalconst_wrap.c: In function ‘PyInit__gdalconst’:
#11 15.20       extensions/gdalconst_wrap.c:3710:3: warning: ‘PyEval_InitThreads’ is deprecated [-Wdeprecated-declarations]
#11 15.20        3710 |   SWIG_PYTHON_INITIALIZE_THREADS;
#11 15.20             |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#11 15.20       In file included from /usr/local/include/python3.9/Python.h:140,
#11 15.20                        from extensions/gdalconst_wrap.c:156:
#11 15.20       /usr/local/include/python3.9/ceval.h:130:37: note: declared here
#11 15.20         130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
#11 15.20             |                                     ^~~~~~~~~~~~~~~~~~
#11 15.20       extensions/osr_wrap.cpp: In function ‘PyObject* PyInit__osr()’:
#11 15.20       extensions/osr_wrap.cpp:982:65: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations]
#11 15.20         982 | #     define SWIG_PYTHON_INITIALIZE_THREADS  PyEval_InitThreads()
#11 15.20             |                                                                 ^
#11 15.20       extensions/osr_wrap.cpp:19126:3: note: in expansion of macro ‘SWIG_PYTHON_INITIALIZE_THREADS’
#11 15.20       19126 |   SWIG_PYTHON_INITIALIZE_THREADS;
#11 15.20             |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#11 15.20       In file included from /usr/local/include/python3.9/Python.h:140,
#11 15.20                        from extensions/osr_wrap.cpp:180:
#11 15.20       /usr/local/include/python3.9/ceval.h:130:37: note: declared here
#11 15.20         130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
#11 15.20             |                                     ^~~~~~~~~~~~~~~~~~
#11 15.20       extensions/gnm_wrap.cpp: In function ‘PyObject* PyInit__gnm()’:
#11 15.20       extensions/gnm_wrap.cpp:982:65: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations]
#11 15.20         982 | #     define SWIG_PYTHON_INITIALIZE_THREADS  PyEval_InitThreads()
#11 15.20             |                                                                 ^
#11 15.20       extensions/gnm_wrap.cpp:6539:3: note: in expansion of macro ‘SWIG_PYTHON_INITIALIZE_THREADS’
#11 15.20        6539 |   SWIG_PYTHON_INITIALIZE_THREADS;
#11 15.20             |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#11 15.20       In file included from /usr/local/include/python3.9/Python.h:140,
#11 15.20                        from extensions/gnm_wrap.cpp:180:
#11 15.20       /usr/local/include/python3.9/ceval.h:130:37: note: declared here
#11 15.20         130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
#11 15.20             |                                     ^~~~~~~~~~~~~~~~~~
#11 15.20       gcc -pthread -shared build/temp.linux-x86_64-3.9/extensions/gdalconst_wrap.o -L../../.libs -L../../ -L/usr/local/lib -L/usr/lib -lgdal -o build/lib.linux-x86_64-3.9/osgeo/_gdalconst.cpython-39-x86_64-linux-gnu.so
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libc.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libc.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libc.so.6 when searching for /lib/x86_64-linux-gnu/libc.so.6
#11 15.20       /usr/bin/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2
#11 15.20       /usr/bin/ld: cannot find /lib64/ld-linux-x86-64.so.2
#11 15.20       /usr/bin/ld: /lib64/ld-linux-x86-64.so.2: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib64/ld-linux-x86-64.so.2 when searching for /lib64/ld-linux-x86-64.so.2
#11 15.20       collect2: error: ld returned 1 exit status
#11 15.20       extensions/ogr_wrap.cpp: In function ‘PyObject* PyInit__ogr()’:
#11 15.20       extensions/ogr_wrap.cpp:982:65: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations]
#11 15.20         982 | #     define SWIG_PYTHON_INITIALIZE_THREADS  PyEval_InitThreads()
#11 15.20             |                                                                 ^
#11 15.20       extensions/ogr_wrap.cpp:36970:3: note: in expansion of macro ‘SWIG_PYTHON_INITIALIZE_THREADS’
#11 15.20       36970 |   SWIG_PYTHON_INITIALIZE_THREADS;
#11 15.20             |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#11 15.20       In file included from /usr/local/include/python3.9/Python.h:140,
#11 15.20                        from extensions/ogr_wrap.cpp:180:
#11 15.20       /usr/local/include/python3.9/ceval.h:130:37: note: declared here
#11 15.20         130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
#11 15.20             |                                     ^~~~~~~~~~~~~~~~~~
#11 15.20       extensions/gdal_wrap.cpp: In function ‘PyObject* PyInit__gdal()’:
#11 15.20       extensions/gdal_wrap.cpp:982:65: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations]
#11 15.20         982 | #     define SWIG_PYTHON_INITIALIZE_THREADS  PyEval_InitThreads()
#11 15.20             |                                                                 ^
#11 15.20       extensions/gdal_wrap.cpp:46157:3: note: in expansion of macro ‘SWIG_PYTHON_INITIALIZE_THREADS’
#11 15.20       46157 |   SWIG_PYTHON_INITIALIZE_THREADS;
#11 15.20             |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#11 15.20       In file included from /usr/local/include/python3.9/Python.h:140,
#11 15.20                        from extensions/gdal_wrap.cpp:180:
#11 15.20       /usr/local/include/python3.9/ceval.h:130:37: note: declared here
#11 15.20         130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
#11 15.20             |                                     ^~~~~~~~~~~~~~~~~~
#11 15.20       g++ -pthread -shared build/temp.linux-x86_64-3.9/extensions/gnm_wrap.o -L../../.libs -L../../ -L/usr/local/lib -L/usr/lib -lgdal -o build/lib.linux-x86_64-3.9/osgeo/_gnm.cpython-39-x86_64-linux-gnu.so
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       collect2: error: ld returned 1 exit status
#11 15.20       g++ -pthread -shared build/temp.linux-x86_64-3.9/extensions/osr_wrap.o -L../../.libs -L../../ -L/usr/local/lib -L/usr/lib -lgdal -o build/lib.linux-x86_64-3.9/osgeo/_osr.cpython-39-x86_64-linux-gnu.so
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       collect2: error: ld returned 1 exit status
#11 15.20       g++ -pthread -shared build/temp.linux-x86_64-3.9/extensions/ogr_wrap.o -L../../.libs -L../../ -L/usr/local/lib -L/usr/lib -lgdal -o build/lib.linux-x86_64-3.9/osgeo/_ogr.cpython-39-x86_64-linux-gnu.so
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       collect2: error: ld returned 1 exit status
#11 15.20       g++ -pthread -shared build/temp.linux-x86_64-3.9/extensions/gdal_wrap.o -L../../.libs -L../../ -L/usr/local/lib -L/usr/lib -lgdal -o build/lib.linux-x86_64-3.9/osgeo/_gdal.cpython-39-x86_64-linux-gnu.so
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libm.so.6: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libm.so.6 when searching for /lib/x86_64-linux-gnu/libm.so.6
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: cannot find /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       /usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
#11 15.20       /usr/bin/ld: skipping incompatible /lib/x86_64-linux-gnu/libmvec.so.1 when searching for /lib/x86_64-linux-gnu/libmvec.so.1
#11 15.20       collect2: error: ld returned 1 exit status
#11 15.20       error: command '/usr/bin/g++' failed with exit code 1
#11 15.20       [end of output]
#11 ERROR: executor failed running [/bin/sh -c pip3 install --no-cache-dir GDAL==3.5.0]: exit code: 1

Tags: docker g++gcc gdal python

Answers

- Tuxette
- November 11, 2022 at 11:50 am
- 0 votes
0
I have the same problem with the exact same error
```
/usr/bin/ld: /lib/x86_64-linux-gnu/libmvec.so.1: unknown type [0x13] section `.relr.dyn'
```
in a container installing the R package "bit" that used to be perfectly functional a few days ago. I think that it is related to this: https://www.mail-archive.com/[email protected]/msg61461.html so if you find a solution, I would be glad to know it.
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- Serge
- December 25, 2022 at 12:10 am
- 0 votes
0
Followed solution that was mentioned in the mailing list and installed binutils.
```
sudo apt install binutils
```
That worked for me.
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Failing to install GDAL on python:3.9 as of Nov 8th – Docker

Answers