tdboer
May 18, 2022, 10:03pm
#1
Hi all,
I am trying to install LSST stack using the newinstall.sh instruction found here: Install with newinstall.sh and eups distrib .
The initial EUPS framework setup works fine, but when I try to get the actual lsst_distrib installed using eups distrib install -t v23_0_1 lsst_distrib The installation fails at the installation of the eigen package. I get the following error snippet:
[ 2/83 ] eigen g398bedf734 ...
***** error: from /home/panstarrs/tdeboer/lsst_stack/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/build.log:
CMake that the project does not need compatibility with older versions.
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11 - Success
-- Performing Test COMPILER_SUPPORT_std=cpp03
-- Performing Test COMPILER_SUPPORT_std=cpp03 - Success
-- Performing Test standard_math_library_linked_to_automatically
-- Performing Test standard_math_library_linked_to_automatically - Failed
-- Performing Test standard_math_library_linked_to_as_m
-- Performing Test standard_math_library_linked_to_as_m - Failed
CMake Error at CMakeLists.txt:111 (message):
Can't link to the standard math library. Please report to the Eigen
developers, telling them about your platform.
-- Configuring incomplete, errors occurred!
It seems the standard math libm library is not being linked in eups? Is there any easy way around this, within eups?
ktl
May 18, 2022, 10:33pm
#2
Can you tell us which OS (and perhaps CPU architecture) you are running under (e.g. the output of uname -a)? And give the value of the EUPS_PKGROOT environment variable?
While we’re figuring this out, you may find that lsstinstallcurl -LO https://ls.st/lsstinstall; bash lsstinstall -T v23_0_1) works better.
tdboer
May 18, 2022, 11:49pm
#3
right right, that is all info I should have given at the start. This machine is running Ubuntu 18.04
uname -a output:
Linux **** 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 23:07:57 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
The EUPS_PKGROOT variable is set to:
https://eups.lsst.codes/stack/src
In the meantime, I will try to install using the lsstinstall instead. See how that goes.
ktl
May 19, 2022, 12:46am
#4
I was successful at building eigen from v23_0_1 in an Ubuntu 18.04 container (with curl and patch installed). Do you have anything that could be overriding GXX, CMAKE_ARGS, CXXFLAGS, CONDA_BUILD_SYSROOT, LD, or LDFLAGS? Just to be sure, could you attach the output of conda info and conda list?
tdboer
May 19, 2022, 1:28am
#5
As far as I can tell, there is nothing that overrides GXX, CMAKE_ARGS, CXXFLAGS, CONDA_BUILD_SYSROOT, LD, or LDFLAGS.
As for the output, I have the following:
conda list:
active environment : base
active env location : /home/panstarrs/tdeboer/anaconda3
shell level : 1
user config file : /home/panstarrs/tdeboer/.condarc
populated config files :
conda version : 4.8.2
conda-build version : 3.18.11
python version : 3.7.6.final.0
virtual packages : __glibc=2.27
base environment : /home/panstarrs/tdeboer/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/panstarrs/tdeboer/anaconda3/pkgs
/home/panstarrs/tdeboer/.conda/pkgs
envs directories : /home/panstarrs/tdeboer/anaconda3/envs
/home/panstarrs/tdeboer/.conda/envs
platform : linux-64
user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Linux/4.15.0-151-generic ubuntu/18.04.5 glibc/2.27
UID:GID : 2697:100
netrc file : None
offline mode : False
conda info:
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py37_0
_libgcc_mutex 0.1 main
alabaster 0.7.12 py37_0
anaconda 2020.02 py37_0
anaconda-client 1.7.2 py37_0
anaconda-navigator 1.9.12 py37_0
anaconda-project 0.8.4 py_0
argh 0.26.2 py37_0
asn1crypto 1.3.0 py37_0
astroid 2.3.3 py37_0
astropy 4.0 py37h7b6447c_0
atomicwrites 1.3.0 py37_1
attrs 19.3.0 py_0
autopep8 1.4.4 py_0
babel 2.8.0 py_0
backcall 0.1.0 py37_0
backports 1.0 py_2
backports.functools_lru_cache 1.6.1 py_0
backports.shutil_get_terminal_size 1.0.0 py37_2
backports.tempfile 1.0 py_1
backports.weakref 1.0.post1 py_1
beautifulsoup4 4.8.2 py37_0
bitarray 1.2.1 py37h7b6447c_0
bkcharts 0.2 py37_0
blas 1.0 mkl
bleach 3.1.0 py37_0
blosc 1.16.3 hd408876_0
bokeh 1.4.0 py37_0
boto 2.49.0 py37_0
bottleneck 1.3.2 py37heb32a55_0
bzip2 1.0.8 h7b6447c_0
ca-certificates 2020.1.1 0
cairo 1.14.12 h8948797_3
certifi 2019.11.28 py37_0
cffi 1.14.0 py37h2e261b9_0
chardet 3.0.4 py37_1003
click 7.0 py37_0
cloudpickle 1.3.0 py_0
clyent 1.2.2 py37_1
colorama 0.4.3 py_0
conda 4.8.2 py37_0
conda-build 3.18.11 py37_0
conda-env 2.6.0 1
conda-package-handling 1.6.0 py37h7b6447c_0
conda-verify 3.4.2 py_1
contextlib2 0.6.0.post1 py_0
cryptography 2.8 py37h1ba5d50_0
curl 7.68.0 hbc83047_0
cycler 0.10.0 py37_0
cython 0.29.15 py37he6710b0_0
cytoolz 0.10.1 py37h7b6447c_0
dask 2.11.0 py_0
dask-core 2.11.0 py_0
dbus 1.13.12 h746ee38_0
decorator 4.4.1 py_0
defusedxml 0.6.0 py_0
diff-match-patch 20181111 py_0
distributed 2.11.0 py37_0
docutils 0.16 py37_0
entrypoints 0.3 py37_0
et_xmlfile 1.0.1 py37_0
expat 2.2.6 he6710b0_0
fastcache 1.1.0 py37h7b6447c_0
filelock 3.0.12 py_0
flake8 3.7.9 py37_0
flask 1.1.1 py_0
fontconfig 2.13.0 h9420a91_0
freetype 2.9.1 h8a8886c_1
fribidi 1.0.5 h7b6447c_0
fsspec 0.6.2 py_0
future 0.18.2 py37_0
get_terminal_size 1.0.0 haa9412d_0
gevent 1.4.0 py37h7b6447c_0
glib 2.63.1 h5a9c865_0
glob2 0.7 py_0
gmp 6.1.2 h6c8ec71_1
gmpy2 2.0.8 py37h10f8cd9_2
graphite2 1.3.13 h23475e2_0
greenlet 0.4.15 py37h7b6447c_0
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.10.0 py37h7918eee_0
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.4 hb1b8bf9_0
heapdict 1.0.1 py_0
html5lib 1.0.1 py37_0
hypothesis 5.5.4 py_0
icu 58.2 h9c2bf20_1
idna 2.8 py37_0
imageio 2.6.1 py37_0
imagesize 1.2.0 py_0
importlib_metadata 1.5.0 py37_0
intel-openmp 2020.0 166
intervaltree 3.0.2 py_0
ipykernel 5.1.4 py37h39e3cac_0
ipython 7.12.0 py37h5ca1d4c_0
ipython_genutils 0.2.0 py37_0
ipywidgets 7.5.1 py_0
isort 4.3.21 py37_0
itsdangerous 1.1.0 py37_0
jbig 2.1 hdba287a_0
jdcal 1.4.1 py_0
jedi 0.14.1 py37_0
jeepney 0.4.2 py_0
jinja2 2.11.1 py_0
joblib 0.14.1 py_0
jpeg 9b h024ee3a_2
json5 0.9.1 py_0
jsonschema 3.2.0 py37_0
jupyter 1.0.0 py37_7
jupyter_client 5.3.4 py37_0
jupyter_console 6.1.0 py_0
jupyter_core 4.6.1 py37_0
jupyterlab 1.2.6 pyhf63ae98_0
jupyterlab_server 1.0.6 py_0
keyring 21.1.0 py37_0
kiwisolver 1.1.0 py37he6710b0_0
krb5 1.17.1 h173b8e3_0
lazy-object-proxy 1.4.3 py37h7b6447c_0
ld_impl_linux-64 2.33.1 h53a641e_7
libarchive 3.3.3 h5d8350f_5
libcurl 7.68.0 h20c2e04_0
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
liblief 0.9.0 h7725739_2
libpng 1.6.37 hbc83047_0
libsodium 1.0.16 h1bed415_0
libspatialindex 1.9.3 he6710b0_0
libssh2 1.8.2 h1ba5d50_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_0
libtool 2.4.6 h7b6447c_5
libuuid 1.0.3 h1bed415_2
libxcb 1.13 h1bed415_1
libxml2 2.9.9 hea5a465_1
libxslt 1.1.33 h7d1a2b0_0
llvmlite 0.31.0 py37hd408876_0
locket 0.2.0 py37_1
lxml 4.5.0 py37hefd8a0e_0
lz4-c 1.8.1.2 h14c3975_0
lzo 2.10 h49e0be7_2
markupsafe 1.1.1 py37h7b6447c_0
matplotlib 3.1.3 py37_0
matplotlib-base 3.1.3 py37hef1b27d_0
mccabe 0.6.1 py37_1
mistune 0.8.4 py37h7b6447c_0
mkl 2020.0 166
mkl-service 2.3.0 py37he904b0f_0
mkl_fft 1.0.15 py37ha843d7b_0
mkl_random 1.1.0 py37hd6b4f25_0
mock 4.0.1 py_0
more-itertools 8.2.0 py_0
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.1 hdf1c602_3
mpmath 1.1.0 py37_0
msgpack-python 0.6.1 py37hfd86e86_1
multipledispatch 0.6.0 py37_0
mysqlclient 2.0.3 pypi_0 pypi
navigator-updater 0.2.1 py37_0
nbconvert 5.6.1 py37_0
nbformat 5.0.4 py_0
ncurses 6.2 he6710b0_0
networkx 2.4 py_0
nltk 3.4.5 py37_0
nose 1.3.7 py37_2
notebook 6.0.3 py37_0
numba 0.48.0 py37h0573a6f_0
numexpr 2.7.1 py37h423224d_0
numpy 1.18.1 py37h4f9e942_0
numpy-base 1.18.1 py37hde5b4d6_1
numpydoc 0.9.2 py_0
olefile 0.46 py37_0
openpyxl 3.0.3 py_0
openssl 1.1.1d h7b6447c_4
packaging 20.1 py_0
pandas 1.0.1 py37h0573a6f_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py37_1
pango 1.42.4 h049681c_0
parso 0.5.2 py_0
partd 1.1.0 py_0
patchelf 0.10 he6710b0_0
path 13.1.0 py37_0
path.py 12.4.0 0
pathlib2 2.3.5 py37_0
pathtools 0.1.2 py_1
patsy 0.5.1 py37_0
pcre 8.43 he6710b0_0
pep8 1.7.1 py37_0
pexpect 4.8.0 py37_0
pickleshare 0.7.5 py37_0
pillow 7.0.0 py37hb39fc2d_0
pip 20.0.2 py37_1
pixman 0.38.0 h7b6447c_0
pkginfo 1.5.0.1 py37_0
pluggy 0.13.1 py37_0
ply 3.11 py37_0
prometheus_client 0.7.1 py_0
prompt_toolkit 3.0.3 py_0
psutil 5.6.7 py37h7b6447c_0
ptyprocess 0.6.0 py37_0
py 1.8.1 py_0
py-lief 0.9.0 py37h7725739_2
pycodestyle 2.5.0 py37_0
pycosat 0.6.3 py37h7b6447c_0
pycparser 2.19 py37_0
pycrypto 2.6.1 py37h14c3975_9
pycurl 7.43.0.5 py37h1ba5d50_0
pydocstyle 4.0.1 py_0
pyflakes 2.1.1 py37_0
pygments 2.5.2 py_0
pylint 2.4.4 py37_0
pyodbc 4.0.30 py37he6710b0_0
pyopenssl 19.1.0 py37_0
pyparsing 2.4.6 py_0
pyqt 5.9.2 py37h05f1152_2
pyrsistent 0.15.7 py37h7b6447c_0
pysocks 1.7.1 py37_0
pytables 3.6.1 py37h71ec239_0
pytest 5.3.5 py37_0
pytest-arraydiff 0.3 py37h39e3cac_0
pytest-astropy 0.8.0 py_0
pytest-astropy-header 0.1.2 py_0
pytest-doctestplus 0.5.0 py_0
pytest-openfiles 0.4.0 py_0
pytest-remotedata 0.3.2 py37_0
python 3.7.6 h0371630_2
python-dateutil 2.8.1 py_0
python-jsonrpc-server 0.3.4 py_0
python-language-server 0.31.7 py37_0
python-libarchive-c 2.8 py37_13
pytz 2019.3 py_0
pywavelets 1.1.1 py37h7b6447c_0
pyxdg 0.26 py_0
pyyaml 5.3 py37h7b6447c_0
pyzmq 18.1.1 py37he6710b0_0
qdarkstyle 2.8 py_0
qt 5.9.7 h5867ecd_1
qtawesome 0.6.1 py_0
qtconsole 4.6.0 py_1
qtpy 1.9.0 py_0
readline 7.0 h7b6447c_5
requests 2.22.0 py37_1
ripgrep 11.0.2 he32d670_0
rope 0.16.0 py_0
rtree 0.9.3 py37_0
ruamel_yaml 0.15.87 py37h7b6447c_0
scikit-image 0.16.2 py37h0573a6f_0
scikit-learn 0.22.1 py37hd81dba3_0
scipy 1.4.1 py37h0b6359f_0
seaborn 0.10.0 py_0
secretstorage 3.1.2 py37_0
send2trash 1.5.0 py37_0
setuptools 45.2.0 py37_0
simplegeneric 0.8.1 py37_2
singledispatch 3.4.0.3 py37_0
sip 4.19.8 py37hf484d3e_0
six 1.14.0 py37_0
snappy 1.1.7 hbae5bb6_3
snowballstemmer 2.0.0 py_0
sortedcollections 1.1.2 py37_0
sortedcontainers 2.1.0 py37_0
soupsieve 1.9.5 py37_0
sphinx 2.4.0 py_0
sphinxcontrib 1.0 py37_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 1.2.0 py_0
spyder 4.0.1 py37_0
spyder-kernels 1.8.1 py37_0
sqlalchemy 1.3.13 py37h7b6447c_0
sqlite 3.31.1 h7b6447c_0
statsmodels 0.11.0 py37h7b6447c_0
sympy 1.5.1 py37_0
tbb 2020.0 hfd86e86_0
tblib 1.6.0 py_0
terminado 0.8.3 py37_0
testpath 0.4.4 py_0
tk 8.6.8 hbc83047_0
toolz 0.10.0 py_0
tornado 6.0.3 py37h7b6447c_3
tqdm 4.42.1 py_0
traitlets 4.3.3 py37_0
ujson 1.35 py37h14c3975_0
unicodecsv 0.14.1 py37_0
unixodbc 2.3.7 h14c3975_0
urllib3 1.25.8 py37_0
watchdog 0.10.2 py37_0
wcwidth 0.1.8 py_0
webencodings 0.5.1 py37_1
werkzeug 1.0.0 py_0
wheel 0.34.2 py37_0
widgetsnbextension 3.5.1 py37_0
wrapt 1.11.2 py37h7b6447c_0
wurlitzer 2.0.0 py37_0
xlrd 1.2.0 py37_0
xlsxwriter 1.2.7 py_0
xlwt 1.3.0 py37_0
xmltodict 0.12.0 py_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
yapf 0.28.0 py_0
zeromq 4.3.1 he6710b0_3
zict 1.0.0 py_0
zipp 2.2.0 py_0
zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0
ktl
May 19, 2022, 1:33am
#6
Wait, those conda commands weren’t executed in the lsst-scipipe-0.8.1 environment, were they?
You must have done source loadLSST.bash and activated that environment before trying the eups distrib install command (otherwise eups wouldn’t be defined).
tdboer
May 19, 2022, 1:54am
#7
oh wait, wrong tab… oopsie
here is the actual info:
conda info
active environment : lsst-scipipe-0.8.1
active env location : /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1
shell level : 2
user config file : /home/panstarrs/tdeboer/.condarc
populated config files : /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.8.5.final.0
virtual packages : __linux=4.15.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2 (writable)
conda av data dir : /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/pkgs
/home/panstarrs/tdeboer/.conda/pkgs
envs directories : /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs
/home/panstarrs/tdeboer/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.24.0 CPython/3.8.5 Linux/4.15.0-151-generic ubuntu/18.04.5 glibc/2.27
UID:GID : 2697:100
netrc file : None
offline mode : False
conda list
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_sysroot_linux-64_curr_repodata_hack 3 h5bd9786_13 conda-forge
abseil-cpp 20210324.2 h9c3ff4c_0 conda-forge
alabaster 0.7.12 py_0 conda-forge
alembic 1.7.7 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
apr 1.7.0 h7f98852_5 conda-forge
arrow-cpp 8.0.0 py38hfe422aa_0_cpu conda-forge
asn1crypto 1.5.1 pyhd8ed1ab_0 conda-forge
asteval 0.9.26 pyhd8ed1ab_0 conda-forge
astropy 5.0.4 py38h71d37f0_0 conda-forge
atk-1.0 2.36.0 h3371d22_4 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
autograd 1.3 py_0 conda-forge
aws-c-cal 0.5.11 h95a6274_0 conda-forge
aws-c-common 0.6.2 h7f98852_0 conda-forge
aws-c-event-stream 0.2.7 h3541f99_13 conda-forge
aws-c-io 0.10.5 hfb6a706_0 conda-forge
aws-checksums 0.1.11 ha31a3da_7 conda-forge
aws-sam-translator 1.45.0 pyhd8ed1ab_0 conda-forge
aws-sdk-cpp 1.8.186 hb4091e7_3 conda-forge
aws-xray-sdk 2.9.0 pyhd8ed1ab_0 conda-forge
babel 2.10.1 pyhd8ed1ab_0 conda-forge
backoff 2.0.1 pyhd8ed1ab_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
binutils 2.36.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_9 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
boost 1.74.0 py38h2b96118_5 conda-forge
boost-cpp 1.74.0 h312852a_4 conda-forge
boto3 1.23.2 pyhd8ed1ab_0 conda-forge
botocore 1.26.2 pyhd8ed1ab_0 conda-forge
bottleneck 1.3.4 py38h71d37f0_1 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
brotlipy 0.7.0 py38h0a891b7_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.3.0 h7f98852_0 conda-forge
ca-certificates 2022.5.18 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2022.5.18 py38h578d9bd_0 conda-forge
cffi 1.14.6 py38ha65f79e_0 conda-forge
cfitsio 3.470 hb418390_7 conda-forge
cfn-lint 0.60.0 pyhd8ed1ab_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
cli_helpers 2.2.1 pyhd8ed1ab_0 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
cmake 3.23.1 h5432695_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
compilers 1.3.0 ha770c72_0 conda-forge
conda 4.12.0 py38h578d9bd_0 conda-forge
conda-package-handling 1.8.1 py38h0a891b7_1 conda-forge
configobj 5.0.6 py_0 conda-forge
coverage 6.3.3 py38h0a891b7_0 conda-forge
cryptography 36.0.2 py38h2b5fc30_1 conda-forge
curl 7.83.1 h7bff187_0 conda-forge
cxx-compiler 1.3.0 h4bd325d_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.30 py38hfa26641_0 conda-forge
cytoolz 0.11.2 py38h0a891b7_2 conda-forge
dask-core 2022.5.0 pyhd8ed1ab_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
decorator 4.4.2 py_0 conda-forge
deprecated 1.2.13 pyh6c4a22f_0 conda-forge
docker-py 5.0.3 py38h578d9bd_2 conda-forge
docker-pycreds 0.4.0 py_0 conda-forge
docopt 0.6.2 py_1 conda-forge
documenteer 0.6.9 pyha770c72_1 conda-forge
docutils 0.17.1 py38h578d9bd_2 conda-forge
doxygen 1.9.2 hb166930_0 conda-forge
dustmaps 1.0.9 py38h578d9bd_1 conda-forge
ecdsa 0.17.0 pyhd8ed1ab_0 conda-forge
eigen 3.3.9 h4bd325d_1 conda-forge
esutil 0.6.9 py38h43a58ef_1 conda-forge
eups 2.2.4 py38h578d9bd_4 conda-forge
execnet 1.9.0 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
fastavro 1.4.12 py38h0a891b7_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
firefly-client 2.8.0 pyhd8ed1ab_0 conda-forge
fitsio 1.1.7 py38h6ed6717_0 conda-forge
flake8 3.8.4 py_0 conda-forge
flake8-polyfill 1.0.2 py_0 conda-forge
flask 2.0.3 pyhd8ed1ab_0 conda-forge
flask_cors 3.0.10 pyhd3deb0d_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.33.3 py38h0a891b7_0 conda-forge
fortran-compiler 1.3.0 h1990efc_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
fsspec 2022.3.0 pyhd8ed1ab_0 conda-forge
future 0.18.2 py38h578d9bd_5 conda-forge
galsim 2.2.6 py38h5714cf5_0 conda-forge
gcc 9.4.0 h192d537_9 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_16 conda-forge
gcc_linux-64 9.4.0 h391b98a_9 conda-forge
gdk-pixbuf 2.42.6 h04a7f16_0 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
gfortran 9.4.0 h2018a41_9 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_16 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_9 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git 2.35.3 pl5321h36853c3_0 conda-forge
git-lfs 3.1.4 ha770c72_0 conda-forge
gitdb 4.0.9 pyhd8ed1ab_0 conda-forge
gitpython 3.1.27 pyhd8ed1ab_0 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.49.1 h85b4f2f_0 conda-forge
greenlet 1.1.2 py38hfa26641_2 conda-forge
grpc-cpp 1.43.2 h9e046d8_3 conda-forge
gsl 2.7 he838d99_0 conda-forge
gtk2 2.24.33 h539f30e_1 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
gxx 9.4.0 h192d537_9 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_16 conda-forge
gxx_linux-64 9.4.0 h0316aca_9 conda-forge
h5py 3.6.0 nompi_py38hfbb2109_100 conda-forge
harfbuzz 3.0.0 h83ec7ef_1 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
healpy 1.15.0 py38hcad0ea4_2 conda-forge
healsparse 1.4.1 pyhd8ed1ab_0 conda-forge
icu 68.2 h9c3ff4c_0 conda-forge
idds-client 0.10.9 pyhd8ed1ab_0 conda-forge
idds-common 0.10.9 pyhd8ed1ab_0 conda-forge
idds-doma 0.10.9 pyhd8ed1ab_0 conda-forge
idds-workflow 0.10.9 pyhd8ed1ab_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagecodecs-lite 2019.12.3 py38h71d37f0_5 conda-forge
imageio 2.19.2 pyhcf75d05_0 conda-forge
imagesize 1.3.0 pyhd8ed1ab_0 conda-forge
iminuit 2.11.2 py38hfa26641_1 conda-forge
importlib-metadata 4.11.3 py38h578d9bd_1 conda-forge
importlib_metadata 4.11.3 hd8ed1ab_1 conda-forge
importlib_resources 3.3.1 pyhd8ed1ab_1 conda-forge
inflection 0.5.1 pyh9f0ad1d_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jinja2 3.0.3 pyhd8ed1ab_0 conda-forge
jmespath 1.0.0 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_1 conda-forge
jq 1.6 h36c2ea0_1000 conda-forge
jschema-to-python 1.2.3 pyhd8ed1ab_0 conda-forge
jsondiff 2.0.0 pyhd8ed1ab_0 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpickle 2.2.0 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge
junit-xml 1.9 pyh9f0ad1d_0 conda-forge
kernel-headers_linux-64 3.10.0 h4a8ded7_13 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.2 py38h43d8883_1 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
latexcodec 2.0.1 pyh9f0ad1d_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libapr 1.7.0 h7f98852_5 conda-forge
libapriconv 1.2.2 h7f98852_5 conda-forge
libaprutil 1.6.1 h975c496_5 conda-forge
libblas 3.9.0 14_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcblas 3.9.0 14_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_16 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgd 2.3.3 h6ad9fb6_0 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.68.4 h3e27bee_0 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libgoogle-cloud 1.36.0 h6945097_0 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 14_linux64_openblas conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 14.3 hd77ab85_0 conda-forge
libprotobuf 3.19.4 h780b84a_0 conda-forge
librsvg 2.52.2 hc3c00ef_0 conda-forge
libsanitizer 9.4.0 h79bfe98_16 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_16 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libthrift 0.16.0 h519c5ea_1 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libutf8proc 2.7.0 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.43.0 h7f98852_0 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
lmfit 1.0.2 pyhd8ed1ab_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
log4cxx 0.11.0 h291d653_3 conda-forge
lsst-dd-rtd-theme 0.2.4 pyhd8ed1ab_0 conda-forge
lsst-documenteer-pipelines 0.6.9 ha770c72_1 conda-forge
lsst-documenteer-technote 0.6.9 ha770c72_1 conda-forge
lsst-sphinx-bootstrap-theme 0.2.2 py_0 conda-forge
lsstdesc.coord 1.2.2 py38h1fd1430_1 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mako 1.2.0 pyhd8ed1ab_1 conda-forge
markupsafe 2.1.1 py38h0a891b7_1 conda-forge
matplotlib-base 3.5.2 py38h826bfd8_0 conda-forge
mccabe 0.6.1 py_1 conda-forge
minuit2 6.22.06 minuit2_standalone conda-forge
minuit2_standalone 6.22.06 h9c3ff4c_100 conda-forge
mock 4.0.3 py38h578d9bd_3 conda-forge
moto 2.3.2 pyhd8ed1ab_0 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.1.3 py38he865349_0 conda-forge
mpich 3.4.3 h846660c_101 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
ndarray 1.6.1 he44f83b_1 conda-forge
networkx 2.5.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.8.0 py38h97b1c41_102 conda-forge
numpy 1.20.3 py38h8246c76_2 conda-forge
numpydoc 1.3.1 pyhd8ed1ab_0 conda-forge
oniguruma 6.9.7.1 h7f98852_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1o h166bdaf_0 conda-forge
orc 1.7.3 h1be678f_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
panda-client 1.5.13 pyhd8ed1ab_0 conda-forge
pandas 1.2.5 py38h1abd341_0 conda-forge
pango 1.48.10 h54213e6_2 conda-forge
parquet-cpp 1.5.1 2 conda-forge
partd 1.2.0 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pbr 5.9.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
pendulum 2.1.2 py38h0a891b7_4 conda-forge
pep8-naming 0.11.1 pyh9f0ad1d_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pgcli 3.4.1 pyhd8ed1ab_0 conda-forge
pgplot 5.2.2 h68245ad_1008 conda-forge
pgspecial 1.13.1 pyhd8ed1ab_0 conda-forge
piff 1.0.0 py38h578d9bd_1 conda-forge
pillow 9.1.1 py38h0ee0e06_0 conda-forge
pip 22.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pluggy 1.0.0 py38h578d9bd_3 conda-forge
prmon 3.0.1 h28135ee_1 conda-forge
progressbar2 4.0.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.29 pyha770c72_0 conda-forge
prompt_toolkit 3.0.29 hd8ed1ab_0 conda-forge
psutil 5.9.0 py38h0a891b7_1 conda-forge
psycopg2 2.9.3 py38h497a2fe_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pyarrow 8.0.0 py38h9f6a473_0_cpu conda-forge
pyasn1 0.4.8 py_0 conda-forge
pybind11 2.9.2 py38h43d8883_1 conda-forge
pybind11-global 2.9.2 py38h43d8883_1 conda-forge
pybtex 0.24.0 pyhd8ed1ab_2 conda-forge
pybtex-docutils 1.0.1 py38h578d9bd_1 conda-forge
pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge
pycosat 0.6.3 py38h0a891b7_1010 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.9.0 py38h0a891b7_1 conda-forge
pyerfa 2.0.0.1 py38h71d37f0_2 conda-forge
pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pyjwt 2.4.0 pyhd8ed1ab_0 conda-forge
pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py38h0a891b7_1 conda-forge
pysocks 1.7.1 py38h578d9bd_5 conda-forge
pytables 3.6.1 py38hdb04529_5 conda-forge
pytest 7.1.2 py38h578d9bd_0 conda-forge
pytest-cov 3.0.0 pyhd8ed1ab_0 conda-forge
pytest-doctestplus 0.12.0 pyhd8ed1ab_0 conda-forge
pytest-flake8 1.1.0 pyhd8ed1ab_0 conda-forge
pytest-forked 1.4.0 pyhd8ed1ab_0 conda-forge
pytest-openfiles 0.5.0 py_0 conda-forge
pytest-runner 6.0.0 pyhd8ed1ab_0 conda-forge
pytest-session2file 0.1.11 pyh44b312d_0 conda-forge
pytest-subtests 0.7.0 pyhd8ed1ab_0 conda-forge
pytest-xdist 2.5.0 pyhd8ed1ab_0 conda-forge
python 3.8.8 hffdb5ce_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-jose 3.3.0 pyh6c4a22f_1 conda-forge
python-utils 3.2.2 pyhd8ed1ab_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pytzdata 2020.1 pyh9f0ad1d_0 conda-forge
pywavelets 1.3.0 py38h71d37f0_1 conda-forge
pyyaml 6.0 py38h0a891b7_4 conda-forge
re2 2022.02.01 h9c3ff4c_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
responses 0.18.0 pyhd8ed1ab_0 conda-forge
rhash 1.4.1 h7f98852_0 conda-forge
rsa 4.8 pyhd8ed1ab_0 conda-forge
ruamel_yaml 0.15.80 py38h497a2fe_1006 conda-forge
rubin-env 0.8.1 ha770c72_1 conda-forge
rubin-env-nosysroot 0.8.1 h2cc385e_1 conda-forge
s2n 1.0.10 h9b69904_0 conda-forge
s3transfer 0.5.2 pyhd8ed1ab_0 conda-forge
sarif-om 1.0.4 pyhd8ed1ab_0 conda-forge
scikit-image 0.17.2 py38h51da96c_4 conda-forge
scikit-learn 1.1.0 py38hf80bbf7_0 conda-forge
scipy 1.8.0 py38h56a6a73_1 conda-forge
scons 4.3.0 py38h578d9bd_0 conda-forge
seaborn 0.11.2 hd8ed1ab_0 conda-forge
seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge
setproctitle 1.2.3 py38h0a891b7_0 conda-forge
setuptools 59.8.0 py38h578d9bd_1 conda-forge
setuptools-scm 6.4.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
spdlog 1.10.0 h924138e_0 conda-forge
sphinx 4.5.0 pyh6c4a22f_0 conda-forge
sphinx-automodapi 0.14.1 pyhd8ed1ab_1 conda-forge
sphinx-click 4.0.3 pyhd8ed1ab_0 conda-forge
sphinx-jinja 1.1.1 py_0 conda-forge
sphinx-prompt 1.4.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-autoprogram 0.1.5 py_1 conda-forge
sphinxcontrib-bibtex 2.4.2 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-doxylink 1.12.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlalchemy 1.4.36 py38h0a891b7_0 conda-forge
sqlite 3.34.0 h74cdb3f_0 conda-forge
sqlparse 0.4.2 pyhd8ed1ab_0 conda-forge
sshpubkeys 3.1.0 py_0 conda-forge
starlink-ast 9.2.7 h166bdaf_1 conda-forge
statsmodels 0.13.2 py38h6c62de6_0 conda-forge
stomp.py 8.0.1 pyhd8ed1ab_0 conda-forge
sysroot_linux-64 2.17 h4a8ded7_13 conda-forge
tabulate 0.8.9 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2020.6.3 py_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
tqdm 4.64.0 pyhd8ed1ab_0 conda-forge
treecorr 4.2.8 py38hfa26641_0 conda-forge
treegp 0.6.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.2.0 hd8ed1ab_1 conda-forge
typing_extensions 4.2.0 pyha770c72_1 conda-forge
uncertainties 3.1.6 pyhd8ed1ab_0 conda-forge
unicodedata2 14.0.0 py38h0a891b7_1 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wcslib 7.3 h72513aa_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
websocket-client 1.3.2 pyhd8ed1ab_0 conda-forge
werkzeug 2.1.2 pyhd8ed1ab_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.14.1 py38h0a891b7_0 conda-forge
ws4py 0.5.1 py_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xpa 2.1.20 h27087fc_1 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge
by the way, I cannot get lsstinstall to work either. It complains about not being to retrieve the relevant repo:
bash lsstinstall -T v23_0_1
Using existing conda at /home/panstarrs/tdeboer/anaconda3
Selected rubin-env=0.8.1
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
It gets stuck on that one
ktl
May 19, 2022, 2:10am
#8
Hmph. The conda outputs look normal. Can you attach the full contents of $EUPS_PATH/EupsBuildDir/Linux64/eigen-g398bedf734/build.log, please?
For lsstinstall, I think it will eventually work, but your older anaconda will take forever. Instead, to get a newer mamba forge, you’ll have to specify the -P option to lsstinstall.
tdboer
May 19, 2022, 2:29am
#9
The full output of the file is:
+ cd /home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734
+ _EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
+ . /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin/setups.sh
++ export EUPS_SHELL=sh
++ EUPS_SHELL=sh
++ export EUPS_DIR=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups
++ EUPS_DIR=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups
+++ echo /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups
+++ sed -e 's/ /-+-/g'
++ eupslocalpath=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups
+++ /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/bin/python -E -c '
from __future__ import print_function
import sys
pp = []
for d in sys.argv[1].split(":"):
if d and d not in pp:
pp += [d]
if not sys.argv[2] in pp:
pp = [sys.argv[2]] + pp
print(":".join(pp))' /home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1 /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups
++ export EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups:/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
++ EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups:/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
++ _eups_path=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups:/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
+++ /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin/eups_setup DYLD_LIBRARY_PATH= eups -r /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups
++ eval export 'EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups;' export 'SETUP_EUPS='\''eups' LOCAL:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups -f Linux64 -Z '(none)'\'';' 'setup()' '{' eval '`"/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin/eups_setup"' 'DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}"' '"$@"`' ';' '};' 'unsetup()' '{' eval '`"/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin/eups_setup"' 'DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}"' --unsetup '"$@"`' ';' '}'
+++ export EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups
+++ EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups
+++ export 'SETUP_EUPS=eups LOCAL:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups -f Linux64 -Z (none)'
+++ SETUP_EUPS='eups LOCAL:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups -f Linux64 -Z (none)'
++ export 'SETUP_EUPS=eups LOCAL:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups -f (none) -Z (none)'
++ SETUP_EUPS='eups LOCAL:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups -f (none) -Z (none)'
++ export EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups:/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
++ EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/share/eups:/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
++ unset eupslocalpath _eups_path
++ '[' X '!=' X -a -f /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/etc/bash_completion.d/eups ']'
+ '[' X/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1 '!=' X ']'
+ EUPS_PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1
+ tar xzvf /tmp/eups/distrib/eigen_b35nn8uo
eigen-g398bedf734/
eigen-g398bedf734/.github/
eigen-g398bedf734/.github/workflows/
eigen-g398bedf734/.github/workflows/null.yaml
eigen-g398bedf734/.hg_archival.txt
eigen-g398bedf734/.hgeol
eigen-g398bedf734/.hgignore
eigen-g398bedf734/.hgtags
eigen-g398bedf734/.krazy
eigen-g398bedf734/patches/
eigen-g398bedf734/patches/cholmod-longs.patch
eigen-g398bedf734/ups/
eigen-g398bedf734/ups/eigen.cfg
eigen-g398bedf734/ups/eigen.table
eigen-g398bedf734/ups/eupspkg.cfg.sh
eigen-g398bedf734/ups/pkginfo
eigen-g398bedf734/upstream/
eigen-g398bedf734/upstream/eigen-3.3.7.tar.gz
++ find . -maxdepth 1 -type d '!' -name '.*'
++ head -n 1
+ PKGDIR=./eigen-g398bedf734
+ test '!' -z ./eigen-g398bedf734
+ cd ./eigen-g398bedf734
+ [[ ! -e ./ups/eupspkg ]]
+ mkdir -p ./ups
+ ln -s /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/lib/eupspkg.sh ups/eupspkg
+ setup --just --type=build alert_packet g4f04a3420f
++ /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin/eups_setup DYLD_LIBRARY_PATH= --just --type=build alert_packet g4f04a3420f
+ eval export 'PYTHONPATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f/python:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/python:.:/home/panstarrs/tdeboer/Apps/python3/:/home/panstarrs/tdeboer/local/lib/python2.5/site-packages:/home/panstarrs/tdeboer/pyroutines/;' export 'PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f/bin:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin:/home/panstarrs/tdeboer/perl5/bin:/home/panstarrs/tdeboer/Apps/python3/bin:/home/panstarrs/tdeboer/ipp/ipp-ops-20220303-rc-ubuntu.lin64/bin:/home/panstarrs/tdeboer/src/ipp-ops-20220303-rc-ubuntu/psconfig:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/bin:/home/panstarrs/tdeboer/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/usr/lib:/home/panstarrs/tdeboer/Apps:/home/panstarrs/tdeboer/myapps/bin:/home/panstarrs/tdeboer/bin:/home/panstarrs/tdeboer/myapps/genescripts:/home/panstarrs/tdeboer/bin/local;' export 'ALERT_PACKET_DIR=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f;' export 'SETUP_ALERT_PACKET='\''alert_packet' g4f04a3420f -f Linux64 -Z '/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1'\'''
++ export PYTHONPATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f/python:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/python:.:/home/panstarrs/tdeboer/Apps/python3/:/home/panstarrs/tdeboer/local/lib/python2.5/site-packages:/home/panstarrs/tdeboer/pyroutines/
++ PYTHONPATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f/python:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/python:.:/home/panstarrs/tdeboer/Apps/python3/:/home/panstarrs/tdeboer/local/lib/python2.5/site-packages:/home/panstarrs/tdeboer/pyroutines/
++ export PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f/bin:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin:/home/panstarrs/tdeboer/perl5/bin:/home/panstarrs/tdeboer/Apps/python3/bin:/home/panstarrs/tdeboer/ipp/ipp-ops-20220303-rc-ubuntu.lin64/bin:/home/panstarrs/tdeboer/src/ipp-ops-20220303-rc-ubuntu/psconfig:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/bin:/home/panstarrs/tdeboer/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/usr/lib:/home/panstarrs/tdeboer/Apps:/home/panstarrs/tdeboer/myapps/bin:/home/panstarrs/tdeboer/bin:/home/panstarrs/tdeboer/myapps/genescripts:/home/panstarrs/tdeboer/bin/local
++ PATH=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f/bin:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin:/home/panstarrs/tdeboer/perl5/bin:/home/panstarrs/tdeboer/Apps/python3/bin:/home/panstarrs/tdeboer/ipp/ipp-ops-20220303-rc-ubuntu.lin64/bin:/home/panstarrs/tdeboer/src/ipp-ops-20220303-rc-ubuntu/psconfig:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/bin:/home/panstarrs/tdeboer/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/usr/lib:/home/panstarrs/tdeboer/Apps:/home/panstarrs/tdeboer/myapps/bin:/home/panstarrs/tdeboer/bin:/home/panstarrs/tdeboer/myapps/genescripts:/home/panstarrs/tdeboer/bin/local
++ export ALERT_PACKET_DIR=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f
++ ALERT_PACKET_DIR=/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/Linux64/alert_packet/g4f04a3420f
++ export 'SETUP_ALERT_PACKET=alert_packet g4f04a3420f -f Linux64 -Z /home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1'
++ SETUP_ALERT_PACKET='alert_packet g4f04a3420f -f Linux64 -Z /home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1'
+ eups list -s
alert_packet g4f04a3420f current o_latest v23_0_1 v23_0_1_rc4 v23_0_1_rc2 v23_0_1_rc1 v23_0_2_rc1 v23_0_2_rc2 v23_0_1_rc3 v23_0_2_rc3 setup
eups LOCAL:/home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups setup
+ ./ups/eupspkg FLAVOR=Linux64 VERBOSE=0 fetch
+ ./ups/eupspkg FLAVOR=Linux64 VERBOSE=0 prep
eupspkg.prep: unpacking ./upstream/eigen-3.3.7.tar.gz ...
eupspkg.prep: applying ./patches/cholmod-longs.patch ...
+ setup --type=build -k -r .
++ /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/eups/bin/eups_setup DYLD_LIBRARY_PATH= --type=build -k -r .
+ eval export 'EIGEN_DIR=/data/ipphome1.0/home/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734;' export 'SETUP_EIGEN='\''eigen' LOCAL:/data/ipphome1.0/home/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734 -f Linux64 -Z '(none)'\'''
++ export EIGEN_DIR=/data/ipphome1.0/home/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734
++ EIGEN_DIR=/data/ipphome1.0/home/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734
++ export 'SETUP_EIGEN=eigen LOCAL:/data/ipphome1.0/home/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734 -f Linux64 -Z (none)'
++ SETUP_EIGEN='eigen LOCAL:/data/ipphome1.0/home/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734 -f Linux64 -Z (none)'
+ ./ups/eupspkg FLAVOR=Linux64 VERBOSE=0 config
-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/bin/x86_64-conda-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/panstarrs/tdeboer/lsst_Pipe/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.8.1/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11 - Success
-- Performing Test COMPILER_SUPPORT_std=cpp03
-- Performing Test COMPILER_SUPPORT_std=cpp03 - Success
-- Performing Test standard_math_library_linked_to_automatically
-- Performing Test standard_math_library_linked_to_automatically - Failed
-- Performing Test standard_math_library_linked_to_as_m
-- Performing Test standard_math_library_linked_to_as_m - Failed
CMake Error at CMakeLists.txt:111 (message):
Can't link to the standard math library. Please report to the Eigen
developers, telling them about your platform.
-- Configuring incomplete, errors occurred!
See also "/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734/build/CMakeFiles/CMakeOutput.log".
See also "/home/panstarrs/tdeboer/lsst_Pipe/stack/miniconda3-py38_4.9.2-0.8.1/EupsBuildDir/Linux64/eigen-g398bedf734/eigen-g398bedf734/build/CMakeFiles/CMakeError.log".
+ exit -3