Problems with installation of SpineToolbox about spine-toolbox

[PekkaSavolainen]

I think you need to do this too

sudo apt-get install unixodbc-dev

Before

pip install -r requirements.txt

This is in the Troubleshooting section of README.md

Thanks Pekka, that would have been my next guess for trouble! @steffenkaminski, you can also try just running

pip install -r requirements.txt --only-binary psycopg2,pyodbc 

Hi! This a known issue on Linux platforms. Pip tries to install package psycopg2 from sources and for that it needs some libraries.

You could first try

pip install -r requirements.txt --only-binary psycopg2

and if that fails, do first (on Debian/Ubuntu like systems)

apt-get install libpq-dev

[steffenkaminski]

Hi Erkka,

Unfortinately, this does not work yet:

(spinetoolbox) steffen@steffen-NG-VN7-591G-767P:~/SPINE/Spine-Toolbox$ sudo apt-get install libpq-dev
[sudo] password for steffen: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  enchant geoip-database gir1.2-appindicator3-0.1 gir1.2-geocodeglib-1.0
  gnome-software-common libappstream-glib8 libbrlapi0.6 libdvdread4
  libenchant1c2a libfluidsynth1 libgspell-1-1 libgutenprint-common
  libgweather-3-15 libpoppler90 libusbmuxd4 node-is-builtin-module pastebinit
  ubuntu-system-service
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  libpq5
Suggested packages:
  postgresql-doc-12
The following NEW packages will be installed:
  libpq-dev libpq5
0 upgraded, 2 newly installed, 0 to remove and 28 not upgraded.
Need to get 0 B/249 kB of archives.
After this operation, 987 kB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Selecting previously unselected package libpq5:amd64.
(Reading database ... 401493 files and directories currently installed.)
Preparing to unpack .../libpq5_12.2-4_amd64.deb ...
Unpacking libpq5:amd64 (12.2-4) ...
Selecting previously unselected package libpq-dev.
Preparing to unpack .../libpq-dev_12.2-4_amd64.deb ...
Unpacking libpq-dev (12.2-4) ...
Setting up libpq5:amd64 (12.2-4) ...
Setting up libpq-dev (12.2-4) ...
Processing triggers for libc-bin (2.31-0ubuntu9) ...
Processing triggers for man-db (2.9.1-1) ...
(spinetoolbox) steffen@steffen-NG-VN7-591G-767P:~/SPINE/Spine-Toolbox$ pip install -r requirements.txt --only-binary psycopg2
Obtaining file:///home/steffen/SPINE/Spine-Toolbox (from -r requirements.txt (line 8))
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: spinedb_api from git+https://github.com/Spine-project/Spine-Database-API.git#egg=spinedb_api in /home/steffen/ELDEST/Spine-Database-API (from -r requirements.txt (line 1)) (0.7.14)
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Requirement already satisfied: cchardet!=2.1.6 in /home/steffen/anaconda3/envs/spinetoolbox/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (2.1.5)
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  Using cached https://files.pythonhosted.org/packages/2b/c1/53ac685833200eb77ef485c2220dac5bfc255418e660790a9eb5cf3abf25/prompt_toolkit-3.0.7-py3-none-any.whl
Collecting backcall
  Using cached https://files.pythonhosted.org/packages/4c/1c/ff6546b6c12603d8dd1070aa3c3d273ad4c07f5771689a7b69a550e8c951/backcall-0.2.0-py2.py3-none-any.whl
Collecting pickleshare
  Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting s3transfer<0.4.0,>=0.3.0
  Using cached https://files.pythonhosted.org/packages/69/79/e6afb3d8b0b4e96cefbdc690f741d7dd24547ff1f94240c997a26fa908d3/s3transfer-0.3.3-py2.py3-none-any.whl
Collecting botocore<1.18.0,>=1.17.57
  Using cached https://files.pythonhosted.org/packages/b1/31/239d7fed71ab1c4eca938e88e61896d0811e616d73533a21c8e49bf0b785/botocore-1.17.57-py2.py3-none-any.whl
Collecting jmespath<1.0.0,>=0.7.1
  Using cached https://files.pythonhosted.org/packages/07/cb/5f001272b6faeb23c1c9e0acc04d48eaaf5c862c17709d20e3469c6e0139/jmespath-0.10.0-py2.py3-none-any.whl
Collecting ptyprocess>=0.5
  Using cached https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Collecting parso<0.8.0,>=0.7.0
  Using cached https://files.pythonhosted.org/packages/93/d1/e635bdde32890db5aeb2ffbde17e74f68986305a4466b0aa373b861e3f00/parso-0.7.1-py2.py3-none-any.whl
Collecting wcwidth
  Using cached https://files.pythonhosted.org/packages/59/7c/e39aca596badaf1b78e8f547c807b04dae603a433d3e7a7e04d67f2ef3e5/wcwidth-0.2.5-py2.py3-none-any.whl
Collecting docutils<0.16,>=0.10
  Using cached https://files.pythonhosted.org/packages/22/cd/a6aa959dca619918ccb55023b4cb151949c64d4d5d55b3f4ffd7eee0c6e8/docutils-0.15.2-py3-none-any.whl
Building wheels for collected packages: pyodbc
  Building wheel for pyodbc (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/steffen/anaconda3/envs/spinetoolbox/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1d_h2b8f/pyodbc/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1d_h2b8f/pyodbc/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-c42f9aos --python-tag cp37
       cwd: /tmp/pip-install-1d_h2b8f/pyodbc/
  Complete output (15 lines):
  running bdist_wheel
  running build
  running build_ext
  building 'pyodbc' extension
  creating build
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/src
  gcc -pthread -B /home/steffen/anaconda3/envs/spinetoolbox/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPYODBC_VERSION=4.0.30 -I/home/steffen/anaconda3/envs/spinetoolbox/include/python3.7m -c src/buffer.cpp -o build/temp.linux-x86_64-3.7/src/buffer.o -Wno-write-strings
  cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
  In file included from src/buffer.cpp:12:
  src/pyodbc.h:56:10: fatal error: sql.h: No such file or directory
     56 | #include <sql.h>
        |          ^~~~~~~
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyodbc
  Running setup.py clean for pyodbc
Failed to build pyodbc
Installing collected packages: pyodbc, pymysql, jdcal, et-xmlfile, openpyxl, psycopg2, scipy, ipython-genutils, traitlets, jupyter-core, qtpy, tornado, ptyprocess, pexpect, parso, jedi, wcwidth, prompt-toolkit, backcall, pickleshare, pygments, ipython, pyzmq, jupyter-client, ipykernel, qtconsole, unicodecsv, jmespath, docutils, botocore, s3transfer, boto3, xlrd, linear-tsv, jsonlines, tabulator, cached-property, isodate, rfc3986, tableschema, jsonpointer, datapackage, gdxcc, gdx2py, shiboken2, pyside2, cx-Oracle, spinetoolbox
    Running setup.py install for pyodbc ... error
    ERROR: Command errored out with exit status 1:
     command: /home/steffen/anaconda3/envs/spinetoolbox/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1d_h2b8f/pyodbc/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1d_h2b8f/pyodbc/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-rqy1q64r/install-record.txt --single-version-externally-managed --compile
         cwd: /tmp/pip-install-1d_h2b8f/pyodbc/
    Complete output (15 lines):
    running install
    running build
    running build_ext
    building 'pyodbc' extension
    creating build
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/src
    gcc -pthread -B /home/steffen/anaconda3/envs/spinetoolbox/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPYODBC_VERSION=4.0.30 -I/home/steffen/anaconda3/envs/spinetoolbox/include/python3.7m -c src/buffer.cpp -o build/temp.linux-x86_64-3.7/src/buffer.o -Wno-write-strings
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    In file included from src/buffer.cpp:12:
    src/pyodbc.h:56:10: fatal error: sql.h: No such file or directory
       56 | #include <sql.h>
          |          ^~~~~~~
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/steffen/anaconda3/envs/spinetoolbox/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1d_h2b8f/pyodbc/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1d_h2b8f/pyodbc/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-rqy1q64r/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

Im not sure whats failing now.

[steffenkaminski]

Thanks @ererkka @PekkaSavolainen! I could install the toolbox now