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Some packages fail to install from VCS #4768
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I just tried to install it though, it shows different output. How is the result of installing with pip command?
$ pipenv --supportPipenv version: Pipenv location: Python location: Python installations found:
PEP 508 Information:
System environment variables:
Pipenv–specific environment variables: Debug–specific environment variables:
Contents of [[source]]
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"
[packages]
numpy = "*"
cython = "*"
[dev-packages]
[requires]
python_version = "3.9"
Contents of {
"_meta": {
"hash": {
"sha256": "34668d1c10bf734f5daaac2a86eea14d8835a0cc575cb849c3adae26910778d0"
},
"pipfile-spec": 6,
"requires": {
"python_version": "3.9"
},
"sources": [
{
"name": "pypi",
"url": "https://pypi.org/simple",
"verify_ssl": true
}
]
},
"default": {
"cython": {
"hashes": [
"sha256:09ac3087ac7a3d489ebcb3fb8402e00c13d1a3a1c6bc73fd3b0d756a3e341e79",
"sha256:0a142c6b862e6ed6b02209d543062c038c110585b5e32d1ad7c9717af4f07e41",
"sha256:0d414458cb22f8a90d64260da6dace5d5fcebde43f31be52ca51f818c46db8cb",
"sha256:10cb3def9774fa99e4583617a5616874aed3255dc241fd1f4a3c2978c78e1c53",
"sha256:112efa54a58293a4fb0acf0dd8e5b3736e95b595eee24dd88615648e445abe41",
"sha256:166f9f29cd0058ce1a14a7b3a2458b849ed34b1ec5fd4108af3fdd2c24afcbb0",
"sha256:2d9e61ed1056a3b6a4b9156b62297ad18b357a7948e57a2f49b061217696567e",
"sha256:2f41ef7edd76dd23315925e003f0c58c8585f3ab24be6885c4b3f60e77c82746",
"sha256:37bcfa5df2a3009f49624695d917c3804fccbdfcdc5eda6378754a879711a4d5",
"sha256:416046a98255eff97ec02077d20ebeaae52682dfca1c35aadf31260442b92514",
"sha256:4cf4452f0e4d50e11701bca38f3857fe6fa16593e7fd6a4d5f7be66f611b7da2",
"sha256:55b0ee28c2c8118bfb3ad9b25cf7a6cbd724e442ea96956e32ccd908d5e3e043",
"sha256:5dd56d0be50073f0e54825a8bc3393852de0eed126339ecbca0ae149dba55cfc",
"sha256:5fa12ebafc2f688ea6d26ab6d1d2e634a9872509ba7135b902bb0d8b368fb04b",
"sha256:5fb977945a2111f6b64501fdf7ed0ec162cc502b84457fd648d6a558ea8de0d6",
"sha256:60c958bcab0ff315b4036a949bed1c65334e1f6a69e17e9966d742febb59043a",
"sha256:661dbdea519d9cfb288867252b75fef73ffa8e8bb674cec27acf70646afb369b",
"sha256:6a2cf2ccccc25413864928dfd730c29db6f63eaf98206c1e600003a445ca7f58",
"sha256:6ade74eece909fd3a437d9a5084829180751d7ade118e281e9824dd75eafaff2",
"sha256:73ac33a4379056a02031baa4def255717fadb9181b5ac2b244792d53eae1c925",
"sha256:76cbca0188d278e93d12ebdaf5990678e6e436485fdfad49dbe9b07717d41a3c",
"sha256:774cb8fd931ee1ba52c472bc1c19077cd6895c1b24014ae07bb27df59aed5ebe",
"sha256:821c2d416ad7d006b069657ee1034c0e0cb45bdbe9ab6ab631e8c495dfcfa4ac",
"sha256:84826ec1c11cda56261a252ddecac0c7d6b02e47e81b94f40b27b4c23c29c17c",
"sha256:854fe2193d3ad4c8b61932ff54d6dbe10c5fa8749eb8958d72cc0ab28243f833",
"sha256:88dc3c250dec280b0489a83950b15809762e27232f4799b1b8d0bad503f5ab84",
"sha256:8cb87777e82d1996aef6c146560a19270684271c9c669ba62ac6803b3cd2ff82",
"sha256:91339ee4b465924a3ea4b2a9cec7f7227bc4cadf673ce859d24c2b9ef60b1214",
"sha256:9164aeef1af6f837e4fc20402a31d256188ba4d535e262c6cb78caf57ad744f8",
"sha256:a102cfa795c6b3b81a29bdb9dbec545367cd7f353c03e6f30a056fdfefd92854",
"sha256:ad43e684ade673565f6f9d6638015112f6c7f11aa2a632167b79014f613f0f5f",
"sha256:afb521523cb46ddaa8d269b421f88ea2731fee05e65b952b96d4db760f5a2a1c",
"sha256:b28f92e617f540d3f21f8fd479a9c6491be920ffff672a4c61b7fc4d7f749f39",
"sha256:bc05de569f811be1fcfde6756c9048ae518f0c4b6d9f8f024752c5365d934cac",
"sha256:cdf04d07c3600860e8c2ebaad4e8f52ac3feb212453c1764a49ac08c827e8443",
"sha256:d8d1a087f35e39384303f5e6b75d465d6f29d746d7138eae9d3b6e8e6f769eae",
"sha256:eb2843f8cc01c645725e6fc690a84e99cdb266ce8ebe427cf3a680ff09f876aa",
"sha256:f2e9381497b12e8f622af620bde0d1d094035d79b899abb2ddd3a7891f535083",
"sha256:f96411f0120b5cae483923aaacd2872af8709be4b46522daedc32f051d778385"
],
"index": "pypi",
"version": "==0.29.24"
},
"numpy": {
"hashes": [
"sha256:09858463db6dd9f78b2a1a05c93f3b33d4f65975771e90d2cf7aadb7c2f66edf",
"sha256:209666ce9d4a817e8a4597cd475b71b4878a85fa4b8db41d79fdb4fdee01dde2",
"sha256:298156f4d3d46815eaf0fcf0a03f9625fc7631692bd1ad851517ab93c3168fc6",
"sha256:30fc68307c0155d2a75ad19844224be0f2c6f06572d958db4e2053f816b859ad",
"sha256:423216d8afc5923b15df86037c6053bf030d15cc9e3224206ef868c2d63dd6dc",
"sha256:426a00b68b0d21f2deb2ace3c6d677e611ad5a612d2c76494e24a562a930c254",
"sha256:466e682264b14982012887e90346d33435c984b7fead7b85e634903795c8fdb0",
"sha256:51a7b9db0a2941434cd930dacaafe0fc9da8f3d6157f9d12f761bbde93f46218",
"sha256:52a664323273c08f3b473548bf87c8145b7513afd63e4ebba8496ecd3853df13",
"sha256:550564024dc5ceee9421a86fc0fb378aa9d222d4d0f858f6669eff7410c89bef",
"sha256:5de64950137f3a50b76ce93556db392e8f1f954c2d8207f78a92d1f79aa9f737",
"sha256:640c1ccfd56724f2955c237b6ccce2e5b8607c3bc1cc51d3933b8c48d1da3723",
"sha256:7fdc7689daf3b845934d67cb221ba8d250fdca20ac0334fea32f7091b93f00d3",
"sha256:805459ad8baaf815883d0d6f86e45b3b0b67d823a8f3fa39b1ed9c45eaf5edf1",
"sha256:92a0ab128b07799dd5b9077a9af075a63467d03ebac6f8a93e6440abfea4120d",
"sha256:9f2dc79c093f6c5113718d3d90c283f11463d77daa4e83aeeac088ec6a0bda52",
"sha256:a5109345f5ce7ddb3840f5970de71c34a0ff7fceb133c9441283bb8250f532a3",
"sha256:a55e4d81c4260386f71d22294795c87609164e22b28ba0d435850fbdf82fc0c5",
"sha256:a9da45b748caad72ea4a4ed57e9cd382089f33c5ec330a804eb420a496fa760f",
"sha256:b160b9a99ecc6559d9e6d461b95c8eec21461b332f80267ad2c10394b9503496",
"sha256:b342064e647d099ca765f19672696ad50c953cac95b566af1492fd142283580f",
"sha256:b5e8590b9245803c849e09bae070a8e1ff444f45e3f0bed558dd722119eea724",
"sha256:bf75d5825ef47aa51d669b03ce635ecb84d69311e05eccea083f31c7570c9931",
"sha256:c01b59b33c7c3ba90744f2c695be571a3bd40ab2ba7f3d169ffa6db3cfba614f",
"sha256:d96a6a7d74af56feb11e9a443150216578ea07b7450f7c05df40eec90af7f4a7",
"sha256:dd0e3651d210068d13e18503d75aaa45656eef51ef0b261f891788589db2cc38",
"sha256:e167b9805de54367dcb2043519382be541117503ce99e3291cc9b41ca0a83557",
"sha256:e42029e184008a5fd3d819323345e25e2337b0ac7f5c135b7623308530209d57",
"sha256:f545c082eeb09ae678dd451a1b1dbf17babd8a0d7adea02897a76e639afca310",
"sha256:fde50062d67d805bc96f1a9ecc0d37bfc2a8f02b937d2c50824d186aa91f2419"
],
"index": "pypi",
"version": "==1.21.2"
}
},
"develop": {}
}
|
Thanks for looking into this! To reproduce everything, the non-Python dependencies for assimulo need to be installed. Without this, you get the error you see. I'll copy the commands here. |
ARG SUNDIALS_VERSION=2.6.2
RUN apt-get install -y --no-install-recommends \
wget \
cmake \
make \
g++ \
\
&& cd /tmp \
&& wget https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \
&& tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \
&& cd sundials-${SUNDIALS_VERSION} \
&& mkdir build \
&& cd build \
&& cmake .. \
&& make \
&& make install \
\
&& cd /tmp \
&& rm sundials-${SUNDIALS_VERSION}.tar.gz \
&& rm -r sundials-${SUNDIALS_VERSION}
ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
# install Python requirements for assimulo
RUN pipenv install cython numpy scipy matplotlib
ARG ASSIMULO_VERSION=3.2.5
RUN apt-get install -y --no-install-recommends \
g++ \
gfortran \
liblas-dev \
liblapack-dev \
git |
Similar issue with installing
Using pipenv Installation succeeds if done directly with |
@jonrkarr I just tried this on my branch that upgrades to the pip 22.0.4 and got an error message that indicates that something up with the setup.py requiring numpy already be installed:
So then I ran Which is very bad thing to do on them. So I install also So I install Fortran compiler Just tried the new version |
Thanks @matteius for exploring. We can install this package with pip, but not with pipenv. As you correctly pointed out, this package does have additional dependencies which must be installed prior to running pipenv/pip. We are installing the package like this:
Specifically, this is the Dockerfile that we're using: https://github.com/biosimulators/Biosimulators_PySCeS/blob/dev/Dockerfile-base |
@jonrkarr Thanks, I just followed your steps, but unfortuantely when I get to the part where your Dockerfile has pip version: 22.0.4
|
The Dockerfile worked as of a few weeks ago. We may have used any older release of pip. |
I try downgrading numpy but I still get the compiler errors about |
@jonrkarr Since I am clearly having some kind of fortran compilation issues with that library, could you try your build out using this branch of pipenv so we know if there is hope for the new pip resolver and dependencies fixing this particular issue? That branch is: #4969 |
@jonrkarr I am going to close this for now but we can revisit if still an issue -- |
In some cases, its necessary to install packages from VCS. Unfortunately, some packages fail to install without clear explanations.
Issue description
For example, the following command results in the error below
Expected result
The package installs or a clear error message is provided.
Actual result
The command above results in this error:
Steps to replicate
$ pipenv --support
Pipenv version:
'2021.5.29'
Pipenv location:
'/home/jonrkarr/.local/lib/python3.9/site-packages/pipenv'
Python location:
'/usr/bin/python3.9'
Python installations found:
3.9.5
:/usr/bin/python3.9
3.7.5
:/usr/local/bin/python3.7
3.7.5
:/usr/local/bin/python3
3.7.5
:/usr/local/bin/python3.7m
3.7.4
:/opt/gurobi900/linux64/bin/python3.7
3.6.9
:/usr/bin/python3
3.6.9
:/usr/bin/python3.6m
3.6.9
:/usr/bin/python3.6
2.7.17
:/usr/bin/python2.7
2.7.17
:/usr/bin/python2
PEP 508 Information:
System environment variables:
NVM_DIR
LD_LIBRARY_PATH
LS_COLORS
LESSCLOSE
CINNAMON_SLOWDOWN_FACTOR
LANG
GDM_LANG
DISPLAY
GPG_TTY
GTK_OVERLAY_SCROLLING
COLORTERM
NVM_CD_FLAGS
JAVA_HOME
XDG_VTNR
SSH_AUTH_SOCK
MANDATORY_PATH
CLASSPATH
XDG_SESSION_ID
XDG_GREETER_DATA_DIR
USER
DESKTOP_SESSION
GNOME_TERMINAL_SCREEN
DEFAULTS_PATH
QT_QPA_PLATFORMTHEME
PWD
HOME
SSH_AGENT_PID
QT_ACCESSIBILITY
XDG_SESSION_TYPE
GUROBI_HOME
XDG_DATA_DIRS
XDG_SESSION_DESKTOP
GJS_DEBUG_OUTPUT
GTK_MODULES
TERM
SHELL
VTE_VERSION
XDG_SEAT_PATH
NVM_BIN
XDG_CURRENT_DESKTOP
GPG_AGENT_INFO
GNOME_TERMINAL_SERVICE
XDG_SEAT
SHLVL
LANGUAGE
GDMSESSION
GNOME_DESKTOP_SESSION_ID
LOGNAME
DBUS_SESSION_BUS_ADDRESS
XDG_RUNTIME_DIR
XAUTHORITY
XDG_SESSION_PATH
XDG_CONFIG_DIRS
PATH
CINNAMON_VERSION
NVM_INC
GJS_DEBUG_TOPICS
SESSION_MANAGER
CINNAMON_SOFTWARE_RENDERING
LESSOPEN
_
PIP_DISABLE_PIP_VERSION_CHECK
PYTHONDONTWRITEBYTECODE
PIP_SHIMS_BASE_MODULE
PIP_PYTHON_PATH
PYTHONFINDER_IGNORE_UNSUPPORTED
Pipenv–specific environment variables:
Debug–specific environment variables:
PATH
:/home/jonrkarr/.local/share/colomoto/bin:/opt/OpenCOR-2021-05-19:/opt/sbfc-1.3.7:/opt/dockstore:/home/jonrkarr/google-cloud-sdk/bin:/home/jonrkarr/.nvm/versions/node/v12.18.1/bin:/home/jonrkarr/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/gurobi900/linux64/bin:/snap/bin:/opt/BioNetGen-2.6.0:/usr/local/go/bin
SHELL
:/bin/bash
LANG
:en_US.UTF-8
PWD
:/home/jonrkarr/Documents/Biosimulations
Contents of
Pipfile
('/home/jonrkarr/Documents/Biosimulations/Pipfile'):Contents of
Pipfile.lock
('/home/jonrkarr/Documents/Biosimulations/Pipfile.lock'):The text was updated successfully, but these errors were encountered: