Can't install using conda. error: no template named 'unique_ptr' in namespace 'std'

[kelvinu]

I get an error on pip install pdftotext

In file included from pdftotext.cpp:5:
/usr/local/include/poppler/cpp/poppler-page.h:63:10: error: no template named 'unique_ptr' in namespace 'std'
    std::unique_ptr<text_box_data> m_data;
    ~~~~~^
1 error generated.
error: command 'gcc' failed with exit status 1

[jalan]

Can you post the full output, starting from pip install pdftotext and ending where the error occurred? If there wasn't very much output, maybe pip --verbose install pdftotext would be better.

[windtalkerlv]

I am experiencing the same issue, so I did the --verbose install. Here is the output

Collecting pdftotext
  1 location(s) to search for versions of pdftotext:
  * https://pypi.python.org/simple/pdftotext/
  Getting page https://pypi.python.org/simple/pdftotext/
  Looking up "https://pypi.python.org/simple/pdftotext/" in the cache
  Returning cached "301 Moved Permanently" response (ignoring date and etag information)
  Looking up "https://pypi.org/simple/pdftotext/" in the cache
  Current age based on date: 800
  Freshness lifetime from max-age: 600
  Freshness lifetime from request max-age: 600
  Starting new HTTPS connection (1): pypi.org
  "GET /simple/pdftotext/ HTTP/1.1" 304 0
  Analyzing links from page https://pypi.org/simple/pdftotext/
    Found link https://files.pythonhosted.org/packages/d2/cf/b65a7431b1c0eaa54063823d6f083ecd9a2a879646af3d243eb09bc8d0b6/pdftotext-1.0.0.tar.gz#sha256=dc645669e88f138ca4a3f7d1e32e0974d4f051da5dffbbabad7cad62dba7bfc4 (from https://pypi.org/simple/pdftotext/), version: 1.0.0
    Found link https://files.pythonhosted.org/packages/68/62/588c9a70a6c4acc6ec4fbc3c096a99032920c4965c4b231745bbd6e7d9f9/pdftotext-1.1.0.tar.gz#sha256=11536c3b91ea3fcdf9466109f304b897a4c49d25390c3ab231ec70acf6d5786d (from https://pypi.org/simple/pdftotext/), version: 1.1.0
    Found link https://files.pythonhosted.org/packages/16/e3/3b432ac931a7b360899686312145ddc9d0ce7b5ac610eba43c3920937ced/pdftotext-2.0.0.tar.gz#sha256=65b78d9c8858b1e98d6b89a6c83e6dfcdaf0bde014dca89cfe10ced7dc38fc39 (from https://pypi.org/simple/pdftotext/), version: 2.0.0
    Found link https://files.pythonhosted.org/packages/38/99/f247b4b27276f2789744900931d40e312564198a9412e653f3f1bb17def6/pdftotext-2.0.1.tar.gz#sha256=947359bde2f1d158d685414dcfb604a369f3fcee49012baf717a71816045d8ef (from https://pypi.org/simple/pdftotext/), version: 2.0.1
    Found link https://files.pythonhosted.org/packages/05/7c/67643e2c10e99f1ac27eadfd9a3d4e13b920c2e922906aad87152cdc154d/pdftotext-2.0.2.tar.gz#sha256=0b82a9fd255a3f2bf5c861cf9e3174d3c4223e1e441bb060c611dcb4e65c6cb8 (from https://pypi.org/simple/pdftotext/), version: 2.0.2
    Found link https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz#sha256=b7312302007e19fc784263a321b41682f01a582af84e14200cef53b3f4e69a50 (from https://pypi.org/simple/pdftotext/), version: 2.1.0
  Using version 2.1.0 (newest of versions: 1.0.0, 1.1.0, 2.0.0, 2.0.1, 2.0.2, 2.1.0)
  Looking up "https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz" in the cache
  Current age based on date: 1697
  Freshness lifetime from max-age: 365000000
  The response is "fresh", returning cached response
  365000000 > 1697
  Using cached https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz
  Downloading from URL https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz#sha256=b7312302007e19fc784263a321b41682f01a582af84e14200cef53b3f4e69a50 (from https://pypi.org/simple/pdftotext/)
  Running setup.py (path:/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext/setup.py) egg_info for package pdftotext
    Running command python setup.py egg_info
    running egg_info
    creating pip-egg-info/pdftotext.egg-info
    writing pip-egg-info/pdftotext.egg-info/PKG-INFO
    writing dependency_links to pip-egg-info/pdftotext.egg-info/dependency_links.txt
    writing top-level names to pip-egg-info/pdftotext.egg-info/top_level.txt
    writing manifest file 'pip-egg-info/pdftotext.egg-info/SOURCES.txt'
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/pdftotext.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pip-egg-info/pdftotext.egg-info/SOURCES.txt'
  Source in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext has version 2.1.0, which satisfies requirement pdftotext from https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz#sha256=b7312302007e19fc784263a321b41682f01a582af84e14200cef53b3f4e69a50
Installing collected packages: pdftotext
  Running setup.py install for pdftotext ...     Running command /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-jzol2wpc-record/install-record.txt --single-version-externally-managed --compile
    running install
    running build
    running build_ext
    building 'pdftotext' extension
    creating build
    creating build/temp.macosx-10.6-intel-3.6
    /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DPOPPLER_CPP_AT_LEAST_0_30_0=1 -I/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c pdftotext.cpp -o build/temp.macosx-10.6-intel-3.6/pdftotext.o -Wall
    In file included from pdftotext.cpp:5:
    /usr/local/include/poppler/cpp/poppler-page.h:70:10: error: no type named 'unique_ptr' in namespace 'std'
        std::unique_ptr<text_box_data> m_data;
        ~~~~~^
    /usr/local/include/poppler/cpp/poppler-page.h:70:20: error: expected member name or ';' after declaration specifiers
        std::unique_ptr<text_box_data> m_data;
        ~~~~~~~~~~~~~~~^
    2 errors generated.
    error: command '/usr/bin/clang' failed with exit status 1
error
Cleaning up...
  Removing source in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext
Command "/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-jzol2wpc-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext/
Exception information:
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/req/req_set.py", line 784, in install
    **kwargs
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/req/req_install.py", line 878, in install
    spinner=spinner,
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip.exceptions.InstallationError: Command "/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-jzol2wpc-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-p43t__6r/pdftotext/

[jalan]

@windtalkerlv thanks for the detailed output!

creating build/temp.macosx-10.6-intel-3.6

Are you using macOS 10.6, from roughly 2009? It might be that it doesn't support some C++11 features by default. Maybe

CFLAGS="-std=c++11" pip install --verbose pdftotext

will help. Otherwise, maybe it's time to do some updates?

[windtalkerlv]

@jalan thanks for the help! I am using High Sierra 10.13.6, and I tired CFLAGS="-std=c++11" pip install --verbose pdftotext. still same problem. heres the log:

$ CFLAGS="-std=c++11" pip3 install --verbose pdftotext
Collecting pdftotext
  1 location(s) to search for versions of pdftotext:
  * https://pypi.python.org/simple/pdftotext/
  Getting page https://pypi.python.org/simple/pdftotext/
  Looking up "https://pypi.python.org/simple/pdftotext/" in the cache
  Returning cached "301 Moved Permanently" response (ignoring date and etag information)
  Looking up "https://pypi.org/simple/pdftotext/" in the cache
  Current age based on date: 36
  Freshness lifetime from max-age: 600
  Freshness lifetime from request max-age: 600
  The response is "fresh", returning cached response
  600 > 36
  Analyzing links from page https://pypi.org/simple/pdftotext/
    Found link https://files.pythonhosted.org/packages/d2/cf/b65a7431b1c0eaa54063823d6f083ecd9a2a879646af3d243eb09bc8d0b6/pdftotext-1.0.0.tar.gz#sha256=dc645669e88f138ca4a3f7d1e32e0974d4f051da5dffbbabad7cad62dba7bfc4 (from https://pypi.org/simple/pdftotext/), version: 1.0.0
    Found link https://files.pythonhosted.org/packages/68/62/588c9a70a6c4acc6ec4fbc3c096a99032920c4965c4b231745bbd6e7d9f9/pdftotext-1.1.0.tar.gz#sha256=11536c3b91ea3fcdf9466109f304b897a4c49d25390c3ab231ec70acf6d5786d (from https://pypi.org/simple/pdftotext/), version: 1.1.0
    Found link https://files.pythonhosted.org/packages/16/e3/3b432ac931a7b360899686312145ddc9d0ce7b5ac610eba43c3920937ced/pdftotext-2.0.0.tar.gz#sha256=65b78d9c8858b1e98d6b89a6c83e6dfcdaf0bde014dca89cfe10ced7dc38fc39 (from https://pypi.org/simple/pdftotext/), version: 2.0.0
    Found link https://files.pythonhosted.org/packages/38/99/f247b4b27276f2789744900931d40e312564198a9412e653f3f1bb17def6/pdftotext-2.0.1.tar.gz#sha256=947359bde2f1d158d685414dcfb604a369f3fcee49012baf717a71816045d8ef (from https://pypi.org/simple/pdftotext/), version: 2.0.1
    Found link https://files.pythonhosted.org/packages/05/7c/67643e2c10e99f1ac27eadfd9a3d4e13b920c2e922906aad87152cdc154d/pdftotext-2.0.2.tar.gz#sha256=0b82a9fd255a3f2bf5c861cf9e3174d3c4223e1e441bb060c611dcb4e65c6cb8 (from https://pypi.org/simple/pdftotext/), version: 2.0.2
    Found link https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz#sha256=b7312302007e19fc784263a321b41682f01a582af84e14200cef53b3f4e69a50 (from https://pypi.org/simple/pdftotext/), version: 2.1.0
  Using version 2.1.0 (newest of versions: 1.0.0, 1.1.0, 2.0.0, 2.0.1, 2.0.2, 2.1.0)
  Looking up "https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz" in the cache
  Current age based on date: 36
  Freshness lifetime from max-age: 365000000
  The response is "fresh", returning cached response
  365000000 > 36
  Using cached https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz
  Downloading from URL https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz#sha256=b7312302007e19fc784263a321b41682f01a582af84e14200cef53b3f4e69a50 (from https://pypi.org/simple/pdftotext/)
  Running setup.py (path:/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext/setup.py) egg_info for package pdftotext
    Running command python setup.py egg_info
    running egg_info
    creating pip-egg-info/pdftotext.egg-info
    writing pip-egg-info/pdftotext.egg-info/PKG-INFO
    writing dependency_links to pip-egg-info/pdftotext.egg-info/dependency_links.txt
    writing top-level names to pip-egg-info/pdftotext.egg-info/top_level.txt
    writing manifest file 'pip-egg-info/pdftotext.egg-info/SOURCES.txt'
    warning: manifest_maker: standard file '-c' not found

    reading manifest file 'pip-egg-info/pdftotext.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pip-egg-info/pdftotext.egg-info/SOURCES.txt'
  Source in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext has version 2.1.0, which satisfies requirement pdftotext from https://files.pythonhosted.org/packages/96/41/aa31f4a6809eb0574674d6c0cf6bc0e00aaf0ea53c62db8a2d9af50b7cc6/pdftotext-2.1.0.tar.gz#sha256=b7312302007e19fc784263a321b41682f01a582af84e14200cef53b3f4e69a50
Installing collected packages: pdftotext
  Running setup.py install for pdftotext ...     Running command /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-r25jq0_p-record/install-record.txt --single-version-externally-managed --compile
    running install
    running build
    running build_ext
    building 'pdftotext' extension
    creating build
    creating build/temp.macosx-10.6-intel-3.6
    /usr/bin/clang -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -std=c++11 -DPOPPLER_CPP_AT_LEAST_0_30_0=1 -I/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c pdftotext.cpp -o build/temp.macosx-10.6-intel-3.6/pdftotext.o -Wall
    In file included from pdftotext.cpp:5:
    /usr/local/include/poppler/cpp/poppler-page.h:70:10: error: no template named 'unique_ptr' in namespace 'std'
        std::unique_ptr<text_box_data> m_data;
        ~~~~~^
    1 error generated.
    error: command '/usr/bin/clang' failed with exit status 1
error
Cleaning up...
  Removing source in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext
Command "/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-r25jq0_p-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext/
Exception information:
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/commands/install.py", line 342, in run
    prefix=options.prefix_path,
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/req/req_set.py", line 784, in install
    **kwargs
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/req/req_install.py", line 878, in install
    spinner=spinner,
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip.exceptions.InstallationError: Command "/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-r25jq0_p-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/dr/rb1tqvx53kgcwd66dfrvvks00000gn/T/pip-build-3z_fud3b/pdftotext/
You are using pip version 9.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[edwardsdl]

I'm having the same problem. Did you ever find a solution?

[jalan]

It looks like I'll finally have to download this anaconda stuff and give it a try, see what sort of build environment it creates. I hope to have time for it this weekend.

[edwardsdl]

I got it working by setting MACOSX_DEPLOYMENT_TARGET. I have no idea why it matters - the installation worked great for my coworkers.

@kelvinu @windtalkerlv give this a try: MACOSX_DEPLOYMENT_TARGET=10.13 pip install -r requirements.txt (you might have to use something other than 10.13 of course).

[jalan]

Thanks, @edwardsdl, that's a good lead. I'll try to find what minimum setting for MACOSX_DEPLOYMENT_TARGET allows the build to succeed in anaconda and see if I can set that automatically in setup.py.

[jalan]

I added -mmacosx-version-min=10.9 to the compiler flags on macOS, which gets the C++11 features required. I pushed a new release with this change. Tested it out in anaconda on macOS and it works now.

For anyone curious, anaconda seems to be the oddball here, shipping a python distribution that builds for ancient 10.6 by default. The macOS system python2, python2 from brew, and python3 from brew all build for 10.13. 🤷‍♂️