TypeError: not a list about carveme

[cdanielmachado]

Could you please try with python 3.6 ?

There have already been other issues reported with python 3.7

[Russel88]

I get the same error with CPLEX 12.10 and the following conda environment:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
boost-cpp 1.70.0 h8e57a91_2 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
carveme 1.2.2 pypi_0 pypi
certifi 2019.11.28 py36_0 conda-forge
chardet 3.0.4 pypi_0 pypi
cplex 12.10.0.0 pypi_0 pypi
cycler 0.10.0 pypi_0 pypi
diamond 0.9.30 h56fc30b_0 bioconda
framed 0.5.1 pypi_0 pypi
future 0.18.2 pypi_0 pypi
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 pypi_0 pypi
kiwisolver 1.1.0 pypi_0 pypi
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
matplotlib 3.1.3 pypi_0 pypi
mpmath 1.1.0 pypi_0 pypi
ncurses 6.1 hf484d3e_1002 conda-forge
numpy 1.18.1 py36h95a1406_0 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pandas 0.24.2 py36hb3f55d8_1 conda-forge
pip 20.0.2 py36_1 conda-forge
pyparsing 2.4.6 pypi_0 pypi
python 3.6.7 h357f687_1006 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python-libsbml 5.18.0 pypi_0 pypi
pytz 2019.3 py_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 pypi_0 pypi
scipy 1.4.1 pypi_0 pypi
setuptools 45.1.0 py36_0 conda-forge
six 1.14.0 py36_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
sympy 1.5.1 pypi_0 pypi
tk 8.6.10 hed695b0_0 conda-forge
urllib3 1.25.8 pypi_0 pypi
wheel 0.34.2 py36_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge

[SPD20]

Could you please try with python 3.6 ?

There have already been other issues reported with python 3.7

Thanks!!

[SPD20]

I get the same error with CPLEX 12.10 and the following conda environment:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
boost-cpp 1.70.0 h8e57a91_2 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
carveme 1.2.2 pypi_0 pypi
certifi 2019.11.28 py36_0 conda-forge
chardet 3.0.4 pypi_0 pypi
cplex 12.10.0.0 pypi_0 pypi
cycler 0.10.0 pypi_0 pypi
diamond 0.9.30 h56fc30b_0 bioconda
framed 0.5.1 pypi_0 pypi
future 0.18.2 pypi_0 pypi
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 pypi_0 pypi
kiwisolver 1.1.0 pypi_0 pypi
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
matplotlib 3.1.3 pypi_0 pypi
mpmath 1.1.0 pypi_0 pypi
ncurses 6.1 hf484d3e_1002 conda-forge
numpy 1.18.1 py36h95a1406_0 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pandas 0.24.2 py36hb3f55d8_1 conda-forge
pip 20.0.2 py36_1 conda-forge
pyparsing 2.4.6 pypi_0 pypi
python 3.6.7 h357f687_1006 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python-libsbml 5.18.0 pypi_0 pypi
pytz 2019.3 py_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 pypi_0 pypi
scipy 1.4.1 pypi_0 pypi
setuptools 45.1.0 py36_0 conda-forge
six 1.14.0 py36_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
sympy 1.5.1 pypi_0 pypi
tk 8.6.10 hed695b0_0 conda-forge
urllib3 1.25.8 pypi_0 pypi
wheel 0.34.2 py36_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge

Hi, I tried various thing but then 'update all' somehow fixed my issue!!

[Russel88]

I still have problems after updating all packages. Could you send a conda environment file or a list of package versions?

[SPD20]

Ahh okay..try with cplex 12.9. By the way here is the list..hope it helps

_anaconda_depends 2019.03 py36_0
_ipyw_jlab_nb_ext_conf 0.1.0 py36_0
alabaster 0.7.12 py36_0
anaconda custom py36_1
anaconda-client 1.7.2 py36_0
anaconda-navigator 1.9.7 py36_0
anaconda-project 0.8.4 py_0
argh 0.26.2 py36_0
asn1crypto 1.3.0 py36_0
astroid 2.3.3 py36_0
astropy 3.0.2 py36h452e1ab_1
atomicwrites 1.3.0 py36_1
attrs 19.3.0 py_0
autopep8 1.4.4 py_0
babel 2.8.0 py_0
backcall 0.1.0 py36_0
backports 1.0 py_2
backports.os 0.1.1 py36_0
backports.shutil_get_terminal_size 1.0.0 py36_2
bcrypt 3.1.7 py36he774522_0
beautifulsoup4 4.8.2 py36_0
bitarray 1.2.1 py36he774522_0
bkcharts 0.2 py36h7e685f7_0
blas 1.0 mkl
blaze 0.11.3 py36h8a29ca5_0
bleach 3.1.0 py36_0
blosc 1.16.3 h7bd577a_0
bokeh 0.12.16 py36_0
boto 2.49.0 py36_0
bottleneck 1.2.1 py36hd119dfa_0
bzip2 1.0.8 he774522_0
ca-certificates 2020.1.1 0
carveme 1.2.2 pypi_0 pypi
certifi 2019.11.28 py36_0
cffi 1.13.2 py36h7a1dbc1_0
chardet 3.0.4 py36_1003
click 7.0 py36_0
cloudpickle 1.2.2 py_0
clyent 1.2.2 py36_1
colorama 0.4.3 py_0
comtypes 1.1.7 py36_0
conda 4.8.1 py36_0
conda-build 3.18.11 py36_0
conda-env 2.6.0 h36134e3_1
conda-package-handling 1.6.0 py36h62dcd97_0
conda-verify 2.0.0 py36h065de53_0
console_shortcut 0.1.1 3
contextlib2 0.6.0.post1 py_0
cplex 12.8.0.0 pypi_0 pypi
cryptography 2.8 py36h7a1dbc1_0
curl 7.67.0 h2a8f88b_0
cycler 0.10.0 py36h009560c_0
cython 0.29.14 py36ha925a31_0
cytoolz 0.10.1 py36he774522_0
dask 0.17.5 py36_0
dask-core 0.17.5 py36_0
datashape 0.5.4 py36h5770b85_0
decorator 4.4.1 py_0
defusedxml 0.6.0 py_0
diff-match-patch 20181111 py_0
distributed 1.21.8 py36_0
docutils 0.16 py36_0
entrypoints 0.3 py36_0
et_xmlfile 1.0.1 py36h3d2d736_0
fastcache 1.1.0 py36he774522_0
filelock 3.0.12 py_0
flake8 3.7.9 py36_0
flask 1.1.1 py_0
flask-cors 3.0.8 py_0
framed 0.5.1 pypi_0 pypi
freetype 2.8 h51f8f2c_1
future 0.18.2 py36_0
get_terminal_size 1.0.0 h38e98db_0
gevent 1.4.0 py36he774522_0
glob2 0.7 py_0
greenlet 0.4.15 py36hfa6e2cd_0
h5py 2.7.1 py36h3bdd7fb_2
hdf5 1.10.2 hac2f561_1
heapdict 1.0.1 py_0
html5lib 1.0.1 py36_0
icc_rt 2019.0.0 h0cc432a_1
icu 58.2 ha66f8fd_1
idna 2.8 py36_0
imageio 2.3.0 py36_0
imagesize 1.2.0 py_0
importlib_metadata 1.4.0 py36_0
intel-openmp 2019.4 245
intervaltree 3.0.2 py_0
ipykernel 5.1.4 py36h39e3cac_0
ipython 7.11.1 py36h39e3cac_0
ipython_genutils 0.2.0 py36_0
ipywidgets 7.5.1 py_0
isort 4.3.21 py36_0
itsdangerous 1.1.0 py36_0
jdcal 1.4.1 py_0
jedi 0.14.1 py36_0
jinja2 2.10.3 py_0
jpeg 9b hb83a4c4_2
json5 0.8.5 py_0
jsonschema 3.2.0 py36_0
jupyter 1.0.0 py36_7
jupyter_client 5.3.4 py36_0
jupyter_console 6.1.0 py_0
jupyter_core 4.6.1 py36_0
jupyterlab 1.2.5 pyhf63ae98_0
jupyterlab_launcher 0.10.5 py36_0
jupyterlab_server 1.0.6 py_0
keyring 21.1.0 py36_0
kiwisolver 1.1.0 py36ha925a31_0
krb5 1.16.4 hc04afaa_0
lazy-object-proxy 1.4.3 py36he774522_0
libarchive 3.3.3 h0643e63_5
libcurl 7.67.0 h2a8f88b_0
libiconv 1.15 h1df5818_7
liblief 0.9.0 ha925a31_2
libpng 1.6.37 h2a8f88b_0
libsodium 1.0.16 h9d3ae62_0
libspatialindex 1.9.3 h33f27b4_0
libssh2 1.8.2 h7a1dbc1_0
libtiff 4.1.0 h56a325e_0
libxml2 2.9.9 h464c3ec_0
libxslt 1.1.33 h579f668_0
llvmlite 0.23.2 py36he51fdeb_0
locket 0.2.0 py36hfed976d_1
lxml 4.4.2 py36h1350720_0
lz4-c 1.8.1.2 h2fa13f4_0
lzo 2.10 h6df0209_2
m2w64-gcc-libgfortran 5.3.0 6
m2w64-gcc-libs 5.3.0 7
m2w64-gcc-libs-core 5.3.0 7
m2w64-gmp 6.1.0 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
markupsafe 1.1.1 py36he774522_0
matplotlib 2.2.2 py36h153e9ff_1
mccabe 0.6.1 py36_1
menuinst 1.4.16 py36he774522_0
mistune 0.8.4 py36he774522_0
mkl 2018.0.3 1
mkl-service 1.1.2 py36hb217b18_5
mkl_fft 1.0.1 py36h452e1ab_0
mkl_random 1.0.1 py36h9258bd6_0
more-itertools 8.0.2 py_0
mpmath 1.1.0 py36_0
msgpack 0.6.2 pypi_0 pypi
msgpack-python 0.6.1 py36h74a9793_1
msys2-conda-epoch 20160418 1
multipledispatch 0.6.0 py36_0
navigator-updater 0.2.1 py36_0
nbconvert 5.6.1 py36_0
nbformat 5.0.4 py_0
networkx 2.4 py_0
nltk 3.4.5 py36_0
nose 1.3.7 py36_2
notebook 6.0.3 py36_0
numba 0.38.0 py36h830ac7b_0
numexpr 2.6.5 py36hcd2f87e_0
numpy 1.14.3 py36h9fa60d3_1
numpy-base 1.14.3 py36h555522e_1
numpydoc 0.9.2 py_0
odo 0.5.1 py36h7560279_0
olefile 0.46 py36_0
openpyxl 3.0.3 py_0
openssl 1.1.1d he774522_3
packaging 20.1 py_0
pandas 0.23.0 py36h830ac7b_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py36_1
paramiko 2.6.0 py36_0
parso 0.6.0 py_0
partd 1.1.0 py_0
path 13.1.0 py36_0
path.py 12.4.0 0
pathlib2 2.3.5 py36_0
pathtools 0.1.2 py_1
patsy 0.5.0 py36_0
pep8 1.7.1 py36_0
pexpect 4.8.0 py36_0
pickleshare 0.7.5 py36_0
pillow 5.1.0 py36h0738816_0
pip 20.0.2 py36_1
pkginfo 1.5.0.1 py36_0
pluggy 0.13.1 py36_0
ply 3.11 py36_0
powershell_shortcut 0.0.1 2
prometheus_client 0.7.1 py_0
prompt_toolkit 3.0.3 py_0
psutil 5.6.7 py36he774522_0
py 1.8.1 py_0
py-lief 0.9.0 py36ha925a31_2
pycodestyle 2.5.0 py36_0
pycosat 0.6.3 py36he774522_0
pycparser 2.19 py36_0
pycrypto 2.6.1 py36hfa6e2cd_9
pycurl 7.43.0.4 py36h7a1dbc1_0
pydocstyle 4.0.1 py_0
pyflakes 2.1.1 py36_0
pygments 2.5.2 py_0
pylint 2.4.4 py36_0
pynacl 1.3.0 py36h62dcd97_0
pyodbc 4.0.28 py36ha925a31_0
pyopenssl 19.1.0 py36_0
pyparsing 2.4.6 py_0
pyqt 5.9.2 py36h6538335_2
pyqt5 5.9 pypi_0 pypi
pyreadline 2.1 py36_1
pyrsistent 0.15.7 py36he774522_0
pysocks 1.7.1 py36_0
pytables 3.4.3 py36he6f6034_1
pytest 5.3.4 py36_0
pytest-arraydiff 0.2 py36_0
pytest-astropy 0.3.0 py36_0
pytest-doctestplus 0.1.3 py36_0
pytest-openfiles 0.4.0 py_0
pytest-remotedata 0.3.2 py36_0
python 3.6.10 h9f7ef89_0
python-dateutil 2.8.1 py_0
python-jsonrpc-server 0.3.4 py_0
python-language-server 0.31.7 py36_0
python-libarchive-c 2.8 py36_13
python-libsbml 5.18.0 pypi_0 pypi
pytz 2019.3 py_0
pywavelets 0.5.2 py36hc649158_0
pywin32 227 py36he774522_1
pywin32-ctypes 0.2.0 py36_0
pywinpty 0.5.7 py36_0
pyyaml 5.2 py36he774522_0
pyzmq 18.1.0 py36ha925a31_0
qdarkstyle 2.8 py_0
qt 5.9.7 vc14h73c81de_0
qtawesome 0.6.0 py_0
qtconsole 4.6.0 py_1
qtpy 1.9.0 py_0
requests 2.22.0 py36_1
rope 0.16.0 py_0
rtree 0.9.3 py36h21ff451_0
ruamel_yaml 0.15.87 py36he774522_0
scikit-image 0.13.1 py36hfa6e2cd_1
scikit-learn 0.19.1 py36h53aea1b_0
scipy 1.1.0 py36h672f292_0
seaborn 0.8.1 py36h9b69545_0
send2trash 1.5.0 py36_0
setuptools 45.1.0 py36_0
simplegeneric 0.8.1 py36_2
singledispatch 3.4.0.3 py36h17d0c80_0
sip 4.19.8 pypi_0 pypi
six 1.14.0 py36_0
snappy 1.1.7 h777316e_3
snowballstemmer 2.0.0 py_0
sortedcollections 1.1.2 py36_0
sortedcontainers 2.1.0 py36_0
soupsieve 1.9.5 py36_0
sphinx 2.3.1 py_0
sphinxcontrib 1.0 py36_1
sphinxcontrib-applehelp 1.0.1 py_0
sphinxcontrib-devhelp 1.0.1 py_0
sphinxcontrib-htmlhelp 1.0.2 py_0
sphinxcontrib-jsmath 1.0.1 py_0
sphinxcontrib-qthelp 1.0.2 py_0
sphinxcontrib-serializinghtml 1.1.3 py_0
sphinxcontrib-websupport 1.1.2 py_0
spyder 4.0.1 py36_0
spyder-kernels 1.8.1 py36_0
sqlalchemy 1.3.13 py36he774522_0
sqlite 3.30.1 he774522_0
statsmodels 0.9.0 py36h452e1ab_0
sympy 1.5.1 py36_0
tbb 2019.4 h74a9793_0
tbb4py 2019.4 py36h74a9793_0
tblib 1.6.0 py_0
terminado 0.8.3 py36_0
testpath 0.4.4 py_0
tk 8.6.8 hfa6e2cd_0
toolz 0.10.0 py_0
tornado 6.0.3 py36he774522_0
tqdm 4.42.0 py_0
traitlets 4.3.3 py36_0
typed-ast 1.4.1 py36he774522_0
typing 3.6.4 py36_0
ujson 1.35 py36hfa6e2cd_0
unicodecsv 0.14.1 py36h6450c06_0
urllib3 1.25.8 py36_0
vc 14.1 h0510ff6_4
vs2015_runtime 14.16.27012 hf0eaf9b_1
watchdog 0.9.0 py36_1
wcwidth 0.1.7 py36_0
webencodings 0.5.1 py36_1
werkzeug 0.16.1 py_0
wheel 0.34.1 py36_0
widgetsnbextension 3.5.1 py36_0
win_inet_pton 1.1.0 py36_0
win_unicode_console 0.5 py36hcdbd4b5_0
wincertstore 0.2 py36h7fe50ca_0
winpty 0.4.3 4
wrapt 1.11.2 py36he774522_0
xlrd 1.2.0 py36_0
xlsxwriter 1.2.7 py_0
xlwings 0.17.0 py36_0
xlwt 1.3.0 py36h1a4751e_0
xz 5.2.4 h2fa13f4_4
yaml 0.1.7 hc54c509_2
yapf 0.28.0 py_0
zeromq 4.3.1 h33f27b4_3
zict 1.0.0 py_0
zipp 0.6.0 py_0
zlib 1.2.11 h62dcd97_3
zstd 1.3.7 h508b16e_0

[cdanielmachado]

The current stable version of CarveMe should support CPLEX 12.7 with Python 3.6.

I will soon(ish) launch a minor release with updates for python 3.7 and cplex (up to) 12.10.

In the meantime, I apologize and ask for some patience. :)

[Russel88]

Hi Daniel,

Thanks a lot for the details
I got it working with CPLEX 12.8, python 3.6, and pandas 0.24

[cdanielmachado]

Perfect! Sorry for the inconvenience. I will address these versioning issues in the next release.