All Conda environments missing Perl HTML Parser module required to launch PyCBC workflow
Summary
All Conda environments missing Perl HTML Parser module required to launch PyCBC workflow
Steps to reproduce
$ source /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/bin/activate ligo-py36
$ which perl
/cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/envs/ligo-py36/bin/perl
$ perl -e 'use HTML::Entities'
Can't locate HTML/Entities.pm in @INC (you may need to install the HTML::Entities module) (@INC contains: /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/.digests/sha256/0f/0f83d26f7ef48637e5e7e2d58fa9ae1fee270e299621fd748343d0586c3f85d7/envs/ligo-py36/lib/site_perl/5.26.2/x86_64-linux-thread-multi /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/.digests/sha256/0f/0f83d26f7ef48637e5e7e2d58fa9ae1fee270e299621fd748343d0586c3f85d7/envs/ligo-py36/lib/site_perl/5.26.2 /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/.digests/sha256/0f/0f83d26f7ef48637e5e7e2d58fa9ae1fee270e299621fd748343d0586c3f85d7/envs/ligo-py36/lib/5.26.2/x86_64-linux-thread-multi /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/.digests/sha256/0f/0f83d26f7ef48637e5e7e2d58fa9ae1fee270e299621fd748343d0586c3f85d7/envs/ligo-py36/lib/5.26.2 .) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
The module is installed onto the system version of perl, so that I can successfully run:
$ conda deactivate
$ perl -e 'use HTML::Entities'
Environment
Environment (conda list
)💯
$ conda list
# packages in environment at /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/envs/ligo-py36:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
asn1crypto 0.24.0 py36_1003 conda-forge
astroid 2.2.5 py36_0 conda-forge
astroplan 0.5 py36_0 conda-forge
astropy 3.2.1 py36h516909a_0 conda-forge
astropy-healpix 0.4 py36h3010b51_1000 conda-forge
atomicwrites 1.3.0 py_0 conda-forge
attrs 19.1.0 py_0 conda-forge
autoconf 2.69 pl526h14c3975_9 conda-forge
automake 1.16.1 pl526_1003 conda-forge
backcall 0.1.0 py_0 conda-forge
bayeswave 1.0.3 h88e4a8a_1 conda-forge
bayeswaveutils 1.0.3 py36_1 conda-forge
bc 1.06 h14c3975_1001 conda-forge
beautifulsoup4 4.7.1 py36_1001 conda-forge
bilby 0.5.2 0 conda-forge
bilby_pipe 0.2.2 py_1 conda-forge
binutils 1.0.1 0 conda-forge
binutils_impl_linux-64 2.31.1 h6176602_1
binutils_linux-64 2.31.1 h6176602_7
blas 2.10 openblas conda-forge
bleach 3.1.0 py_0 conda-forge
blosc 1.16.3 he1b5a44_1 conda-forge
boost-cpp 1.70.0 ha2d47e9_0 conda-forge
boto 2.49.0 py_0 conda-forge
bruco 0.1.1 py36_0 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
c-compiler 1.0.1 h14c3975_0 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
certifi 2019.6.16 py36_0 conda-forge
cffi 1.12.3 py36h8022711_0 conda-forge
cfitsio 3.470 hb60a0a2_1 conda-forge
chardet 3.0.4 py36_1003 conda-forge
chealpix 3.30.0 h60f8253_1002 conda-forge
click 7.0 py_0 conda-forge
cmake 3.14.5 hf94ab9c_0 conda-forge
coloredlogs 10.0 py36_1000 conda-forge
compilers 1.0.1 0 conda-forge
configargparse 0.13.0 py_1 conda-forge
configobj 5.0.6 py_0 conda-forge
coreutils 8.31 h14c3975_0 conda-forge
corner 2.0.1 py_1001 conda-forge
cryptography 2.7 py36h72c5cf5_0 conda-forge
curl 7.64.1 hf8cf82a_0 conda-forge
cxx-compiler 1.0.1 h6bb024c_0 conda-forge
cycler 0.10.0 py_1 conda-forge
cyrus-sasl 2.1.27 he38ecfd_0 conda-forge
cython 0.29.12 py36he1b5a44_0 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.0 py_0 conda-forge
deepdish 0.3.4 py_3 conda-forge
defusedxml 0.5.0 py_1 conda-forge
dill 0.3.0 py36_0 conda-forge
dnspython 1.15.0 py_0 conda-forge
dqsegdb 1.6.0 py36_0 conda-forge
dqsegdb2 1.0.1 py_0 conda-forge
dynesty 0.9.7 py_0 conda-forge
ecdsa 0.13 py_0 conda-forge
emcee 2.2.1 pyh24bf2e0_4 conda-forge
entrypoints 0.3 py36_1000 conda-forge
expat 2.2.5 he1b5a44_1003 conda-forge
fftw 3.3.8 mpi_openmpi_h6dd7431_1006 conda-forge
flake8 3.7.7 py36_0 conda-forge
flask 0.12.4 py_0 conda-forge
flask-cache 0.13.1 py_1000 conda-forge
flask-sqlalchemy 2.4.0 py_0 conda-forge
flex 2.6.4 hf484d3e_1004 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
fortran-compiler 1.0.1 h0e1e685_0 conda-forge
freetype 2.10.0 he983fc9_0 conda-forge
future 0.17.1 py36_1000 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge
gcc_linux-64 7.3.0 h553295d_7 conda-forge
geos 3.7.2 he1b5a44_1 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
gfortran_impl_linux-64 7.3.0 hdf63c60_1
gfortran_linux-64 7.3.0 h553295d_7
gitdb2 2.0.5 py_0 conda-forge
gitpython 2.1.11 py_0 conda-forge
glib 2.58.3 h6f030ca_1002 conda-forge
gpstime 0.3.2 py36_1000 conda-forge
gsl 2.5 h294904e_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_0 conda-forge
gstreamer 1.14.5 h36ae1b5_0 conda-forge
gwdatafind 1.0.4 py_0 conda-forge
gwdetchar 0.5.2 py36_0 conda-forge
gwosc 0.4.3 py_0 conda-forge
gwpy 0.15.0 py36_0 conda-forge
gwsumm 0.1.5 py36_0 conda-forge
gwtrigfind 0.8.0 py_0 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge
gxx_linux-64 7.3.0 h553295d_7 conda-forge
h5py 2.9.0 nompi_py36hf008753_1102 conda-forge
hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge
healpy 1.12.9 py36h313ec66_0 conda-forge
humanfriendly 4.18 py36_0 conda-forge
humanize 0.5.1 py_1 conda-forge
hveto 0.4.0 py36_1 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py36_1000 conda-forge
importlib_metadata 0.18 py36_0 conda-forge
ipykernel 5.1.1 py36h24bf2e0_0 conda-forge
ipython 7.6.1 py36h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.0 py_0 conda-forge
isort 4.3.21 py36_0 conda-forge
itsdangerous 1.1.0 py_0 conda-forge
jedi 0.14.1 py36_0 conda-forge
jinja2 2.10.1 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.0.1 py36_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.3.1 py_0 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.1.0 py36hc9558a2_0 conda-forge
kombine 0.8.3 py_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
lal 6.20.2 fftw_hce47d02_102 conda-forge
lalapps 6.24.0 py36h88e4a8a_1 conda-forge
lalburst 1.5.2 h88e4a8a_1 conda-forge
lalframe 1.4.5 h516909a_0 conda-forge
lalinference 1.11.1 h9c975d8_1 conda-forge
lalinspiral 1.9.0 h88e4a8a_1 conda-forge
lalmetaio 1.5.1 h516909a_0 conda-forge
lalpulsar 1.18.0 h49f03a1_5 conda-forge
lalsimulation 1.9.1 h88e4a8a_0 conda-forge
lalsuite 6.57 py_1 conda-forge
lazy-object-proxy 1.4.1 py36h516909a_0 conda-forge
ldas-tools-al 2.6.2 hc509bcd_1003 conda-forge
ldas-tools-diskcacheapi 2.6.3 h8b68381_1 conda-forge
ldas-tools-filters 2.6.3 h6bb024c_1000 conda-forge
ldas-tools-frameapi 2.6.3 h7ac6fb7_1001 conda-forge
ldas-tools-framecpp 2.6.5 hc509bcd_1004 conda-forge
ldas-tools-ldasgen 2.6.3 hbc69e8a_1002 conda-forge
libblas 3.8.0 10_openblas conda-forge
libcblas 3.8.0 10_openblas conda-forge
libcurl 7.64.1 hda55be3_0 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libframe 8.33 h516909a_0 conda-forge
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
libiconv 1.15 h516909a_1005 conda-forge
libidn2 2.1.1 h14c3975_0 conda-forge
liblapack 3.8.0 10_openblas conda-forge
liblapacke 3.8.0 10_openblas conda-forge
libntlm 1.4 h14c3975_1002 conda-forge
libopenblas 0.3.6 h6e990d7_4 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.4 hd9ab2ff_1 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.0.10 h57b8799_1003 conda-forge
libunistring 0.9.10 h14c3975_0 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libuv 1.30.1 h516909a_0 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_1 conda-forge
libxslt 1.1.32 hae48121_1003 conda-forge
ligo-common 1.0.3 py_0 conda-forge
ligo-followup-advocate 0.0.28 py_0 conda-forge
ligo-gracedb 2.2.0 py_0 conda-forge
ligo-lvalert 1.5.6 py36_0 conda-forge
ligo-raven 1.10 py_0 conda-forge
ligo-segments 1.2.0 py36h14c3975_0 conda-forge
ligo.skymap 0.1.7 py36h4ad5973_2 conda-forge
ligotimegps 2.0.1 py_0 conda-forge
llvm-openmp 8.0.0 hc9558a2_0 conda-forge
lscsoft-glue 2.0.0 py36h14c3975_0 conda-forge
lxml 4.3.4 py36h7ec2d77_0 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
lzo 2.10 h14c3975_1000 conda-forge
m4 1.4.18 h14c3975_1001 conda-forge
mako 1.0.10 py_0 conda-forge
markuppy 1.14 py_0 conda-forge
markupsafe 1.1.1 py36h14c3975_0 conda-forge
matplotlib 3.1.1 py36_0 conda-forge
matplotlib-base 3.1.1 py36hfd891ef_0 conda-forge
mccabe 0.6.1 py_1 conda-forge
metaio 8.5.1 h84994c4_1000 conda-forge
mistune 0.8.4 py36h14c3975_1000 conda-forge
mock 3.0.5 py36_0 conda-forge
more-itertools 7.1.0 py_0 conda-forge
mpi 1.0 openmpi conda-forge
mpld3 0.3 py_1 conda-forge
nbconvert 5.5.0 py_0 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
nds2-client 0.16.3 hf484d3e_0 conda-forge
networkx 2.3 py_0 conda-forge
notebook 5.7.8 py36_1 conda-forge
numexpr 2.6.9 py36h637b7d7_1000 conda-forge
numpy 1.16.4 py36h95a1406_0 conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.6 h6e990d7_4 conda-forge
openmp 8.0.0 0 conda-forge
openmpi 4.0.1 hc99cbb1_1 conda-forge
openssl 1.1.1c h516909a_0 conda-forge
p_astro 0.7 py_0 conda-forge
packaging 19.0 py_0 conda-forge
pamela 1.0.0 py_0 conda-forge
pandas 0.24.2 py36hb3f55d8_0 conda-forge
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.5.0 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.41 hf484d3e_1003 conda-forge
perl 5.26.2 h516909a_1006 conda-forge
pesummary 0.1.7 py_0 conda-forge
pexpect 4.7.0 py36_0 conda-forge
pickleshare 0.7.5 py36_1000 conda-forge
pillow 6.0.0 py36he7afcd5_0 conda-forge
pip 19.1.1 py36_0 conda-forge
pkg-config 0.29.2 h14c3975_1005 conda-forge
pluggy 0.12.0 py_0 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
psutil 5.6.3 py36h516909a_0 conda-forge
psycopg2 2.8.3 py36h72c5cf5_0 conda-forge
ptemcee 1.0.0 py_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.8.0 py_0 conda-forge
pyasn1 0.4.5 py_0 conda-forge
pyasn1-modules 0.2.5 py_0 conda-forge
pycbc 1.14.0 py36h516909a_1 conda-forge
pycodestyle 2.5.0 py_0 conda-forge
pycondor 0.5.0 py_1 conda-forge
pycparser 2.19 py36_1 conda-forge
pycrypto 2.6.1 py36h14c3975_1002 conda-forge
pyflakes 2.1.1 py_0 conda-forge
pygments 2.4.2 py_0 conda-forge
pykerberos 1.1.14 py36h84109d8_2
pylint 2.3.1 py36_0 conda-forge
pyopenssl 19.0.0 py36_0 conda-forge
pyparsing 2.4.0 py_0 conda-forge
pyqt 5.9.2 py36hcca6a23_0 conda-forge
pyrsistent 0.15.3 py36h516909a_0 conda-forge
pyrxp 2.1.0 py36h14c3975_1000 conda-forge
pysocks 1.7.0 py36_0 conda-forge
pytables 3.5.2 py36ha1aa75f_0 conda-forge
pytest 5.0.1 py36_0 conda-forge
pytest-arraydiff 0.3 py_0 conda-forge
pytest-astropy 0.5.0 py_0 conda-forge
pytest-doctestplus 0.3.0 py_0 conda-forge
pytest-openfiles 0.3.1 py_0 conda-forge
pytest-remotedata 0.3.1 py_0 conda-forge
pytest-runner 5.1 py_0 conda-forge
python 3.6.7 h357f687_1005 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-lal 6.20.2 fftw_py36h18d62be_102 conda-forge
python-lalburst 1.5.2 py36hc1659b7_1 conda-forge
python-lalframe 1.4.5 py36hd352d35_0 conda-forge
python-lalinference 1.11.1 py36h516909a_1 conda-forge
python-lalinspiral 1.9.0 py36hc1659b7_1 conda-forge
python-lalmetaio 1.5.1 py36h516909a_0 conda-forge
python-lalpulsar 1.18.0 py36heade8f8_5 conda-forge
python-lalsimulation 1.9.1 py36h516909a_0 conda-forge
python-ldas-tools-al 2.6.6 py36h6bb024c_1000 conda-forge
python-ldas-tools-framecpp 2.6.8 py36h637b7d7_0 conda-forge
python-ldas-tools-ldasgen 2.6.6 py36h6bb024c_1000 conda-forge
python-ligo-lw 1.5.3 py36h14c3975_0 conda-forge
python-nds2-client 0.16.4 py36h637b7d7_0 conda-forge
python-pegasus-wms 4.9.1 py_0 conda-forge
pytz 2019.1 py_0 conda-forge
pyyaml 5.1.1 py36h516909a_0 conda-forge
pyzmq 18.0.2 py36hc4ba49a_1 conda-forge
qt 5.9.7 h52cfd70_2 conda-forge
qtconsole 4.5.1 py_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
reproject 0.4 py36h3010b51_1000 conda-forge
requests 2.22.0 py36_1 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
scikit-learn 0.19.2 py36h22eb022_0
scipy 1.3.0 py36h921218d_0 conda-forge
seaborn 0.9.0 py_1 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 41.0.1 py36_0 conda-forge
shapely 1.6.4 py36hec07ddf_1006 conda-forge
sip 4.19.8 py36hf484d3e_1000 conda-forge
six 1.12.0 py36_1000 conda-forge
sleekxmpp 1.3.3 py_0 conda-forge
smmap2 2.0.5 py_0 conda-forge
soupsieve 1.9.2 py36_0 conda-forge
sqlalchemy 1.3.5 py36h516909a_0 conda-forge
sqlite 3.29.0 hcee41ef_0 conda-forge
statsmodels 0.10.0 py36hc1659b7_0 conda-forge
swig 4.0.0 he1b5a44_0 conda-forge
terminado 0.8.2 py36_0 conda-forge
testpath 0.4.2 py_1001 conda-forge
tk 8.6.9 hed695b0_1002 conda-forge
tornado 6.0.3 py36h516909a_0 conda-forge
tqdm 4.32.2 py_0 conda-forge
traitlets 4.3.2 py36_1000 conda-forge
typed-ast 1.4.0 py36h516909a_0 conda-forge
urllib3 1.25.3 py36_0 conda-forge
virtualenv 16.0.0 py36_1000 conda-forge
voeventlib 1.2 py_0 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 0.15.4 py_0 conda-forge
wget 1.20.1 h90d6eec_0 conda-forge
wheel 0.33.4 py36_0 conda-forge
widgetsnbextension 3.5.0 py36_0 conda-forge
wrapt 1.11.2 py36h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zipp 0.5.1 py_0 conda-forge
zlib 1.2.11 h516909a_1005 conda-forge
zstd 1.4.0 h3b9ef0a_0 conda-forge
Details about conda
and system ( conda info
):
$ conda info
active environment : ligo-py36
active env location : /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/envs/ligo-py36
shell level : 1
user config file : /home/paul.hopkins/.condarc
populated config files : /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/.condarc
conda version : 4.7.5
conda-build version : 3.18.7
python version : 3.7.3.final.0
virtual packages :
base environment : /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest (read only)
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 : /cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/pkgs
/home/paul.hopkins/.conda/pkgs
envs directories : /home/paul.hopkins/.conda/envs
/cvmfs/ligo-containers.opensciencegrid.org/lscsoft/conda/latest/envs
platform : linux-64
user-agent : conda/4.7.5 requests/2.21.0 CPython/3.7.3 Linux/3.10.0-957.12.2.el7.x86_64 rhel/7.6 glibc/2.17
UID:GID : 100003101:100003101
netrc file : None
offline mode : False
What is the current bug behavior?
It fails to import the module.
What is the expected correct behavior?
It should import the module.
Possible fixes
Do not source Conda environment before using PyCBC Virtual environment.