Comments (2)
kevinrue
commented on June 2, 2024
Somehow, I got it to work (I mean, loading pyBigWig).
Following the advice of a seemingly different issue here ...
Anaconda's curl has troubles when working with https, so that might be the reason why yaourt can't install anything. The command "conda remove curl" leaves you with normal version of curl,
... the last few commands that I ran were:
$ conda remove curl
Fetching package metadata .............
Solving package specifications: .
Package plan for package removal in environment .../miniconda3/envs/py362:
The following packages will be REMOVED:
curl: 7.54.1-0 conda-forge
pybigwig: 0.3.5-np112py36_0 bioconda
Proceed ([y]/n)? y
$pip uninstall pyBigWig
$pip install pyBigWig
which then loaded pyBigWig like a (Py)charm:
>>> import pyBigWig
>>>
For the record, my current environment does not include Anaconda's curl anymore, here is the full list of packages installed right now (while I can import pyBigWig successfully):
$ conda list
# packages in environment at .../miniconda3/envs/py362:
#
alabaster 0.7.10 <pip>
alignlib-lite 0.3 <pip>
Babel 2.5.1 <pip>
biopython 1.70 <pip>
blas 1.1 openblas conda-forge
bleach 2.0.0 <pip>
bokeh 0.12.9 <pip>
brewer2mpl 1.4.1 <pip>
bx-python 0.7.3 <pip>
ca-certificates 2017.7.27.1 0 conda-forge
certifi 2017.7.27.1 py36_0 conda-forge
CGATReport 0.7.6.1 <pip>
cycler 0.10.0 <pip>
Cython 0.26.1 <pip>
decorator 4.1.2 <pip>
docutils 0.14 <pip>
entrypoints 0.2.3 <pip>
et-xmlfile 1.0.1 <pip>
future 0.16.0 <pip>
ggplot 0.11.5 <pip>
html5lib 0.999999999 <pip>
httplib2 0.10.3 <pip>
ipykernel 4.6.1 <pip>
ipython 6.2.0 <pip>
ipython-genutils 0.2.0 <pip>
ipywidgets 7.0.1 <pip>
jedi 0.11.0 <pip>
Jinja2 2.9.6 <pip>
jsonschema 2.6.0 <pip>
jupyter 1.0.0 <pip>
jupyter-client 5.1.0 <pip>
jupyter-console 5.2.0 <pip>
jupyter-core 4.3.0 <pip>
krb5 1.14.2 0 conda-forge
libgfortran 3.0.0 1
libssh2 1.8.0 1 conda-forge
MarkupSafe 1.0 <pip>
matplotlib 2.0.2 <pip>
matplotlib-venn 0.11.5 <pip>
mistune 0.7.4 <pip>
mkl 2017.0.3 0
mpld3 0.3 <pip>
nbconvert 5.3.1 <pip>
nbformat 4.4.0 <pip>
ncurses 5.9 10 conda-forge
networkx 1.11 <pip>
nose 1.3.7 <pip>
notebook 5.1.0 <pip>
numpy 1.12.1 py36_blas_openblas_200 [blas_openblas] conda-forge
numpy 1.13.1 <pip>
olefile 0.44 <pip>
openblas 0.2.19 2 conda-forge
openpyxl 2.5.0a3 <pip>
openssl 1.0.2l 0 conda-forge
pandas 0.20.3 <pip>
pandocfilters 1.4.2 <pip>
parso 0.1.0 <pip>
pep8 1.7.0 <pip>
pexpect 4.2.1 <pip>
pickleshare 0.7.4 <pip>
Pillow 4.2.1 <pip>
pip 9.0.1 py36_0 conda-forge
prompt-toolkit 1.0.15 <pip>
psycopg2 2.7.3.1 <pip>
ptyprocess 0.5.2 <pip>
pybedtools 0.7.10 <pip>
pyBigWig 0.3.5 <pip>
Pygments 2.2.0 <pip>
pyparsing 2.2.0 <pip>
pysam 0.11.1 <pip>
python 3.6.2 0 conda-forge
python-dateutil 2.6.1 <pip>
pytz 2017.2 <pip>
pyzmq 16.0.2 <pip>
qtconsole 4.3.1 <pip>
rdflib 4.2.2 <pip>
readline 6.2 0 conda-forge
requests 2.18.4 <pip>
rpy2 2.9.0 <pip>
ruffus 2.6.3 <pip>
scikit-learn 0.19.0 <pip>
scipy 0.19.1 <pip>
seaborn 0.8.1 <pip>
setuptools 36.3.0 py36_0 conda-forge
setuptools 36.5.0 <pip>
simplegeneric 0.8.1 <pip>
six 1.11.0 <pip>
Sphinx 1.6.3 <pip>
sphinxcontrib-programoutput 0.11 <pip>
sphinxcontrib-websupport 1.0.1 <pip>
SQLAlchemy 1.1.14 <pip>
sqlite 3.13.0 1 conda-forge
statsmodels 0.8.0 <pip>
terminado 0.6 <pip>
testpath 0.3.1 <pip>
tk 8.5.19 2 conda-forge
tornado 4.5.2 <pip>
traitlets 4.3.2 <pip>
urllib3 1.22 <pip>
wcwidth 0.1.7 <pip>
webencodings 0.5.1 <pip>
weblogo 3.5.0 <pip>
wheel 0.30.0 py_1 conda-forge
widgetsnbextension 3.0.3 <pip>
xlwt 1.3.0 <pip>
xz 5.2.3 0 conda-forge
zlib 1.2.11 0 conda-forge
Also, for the sake of completeness, I can confirm that all traces of libcurl have disappeared from
.../miniconda3/envs/py362/lib after conda remove curl. Before the remove, those files were present in the folder:
libcurl.a
libcurl.la
libcurl.so
libcurl.so.4
libcurl.so.4.4.0
Bottom line is that the other issue seems to have nailed the source of the issue: Ananconda's curl. Nothing to fix in pyBigWig as far as I can see.
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dpryan79
commented on June 2, 2024
Weird, there are days when I regret adding support for remote files. Anyway, I'm glad you got things working.
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