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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Problem with samtools : dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib #78

Closed cguetta closed 3 years ago

cguetta commented 3 years ago

Describe the bug I am trying to run velocyto and it requires a lot of additional package and i have a problem with samtools: samtools --version dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/charlotteguetta/opt/anaconda3/bin/samtools Reason: image not found Abort trap: 6

I am on a mac (macOS catalina, version 10.15.7), i have conda (4.10.1). I saw all the other problems people reported previously and i tried them but nothing works... so i decided to create an account and told my issue, hoping that someone will be able to help. i have basic knowledge in programming.

I tried to update samtools but did not work, issue with conda "frozen enviroment" : conda install -c bioconda samtools=1.9=h8ee4bcc_1 openssl=1.0

I also tried the solution with brew, but no difference: brew update= brew install openssl ln -s /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib /usr/local/lib/ ln -s /usr/local/opt/openssl/lib/libssl.1.0.0.dylib /usr/local/lib/

Here is the info from conda list From conda list

Name Version Build Channel

_anaconda_depends 2020.07 py38_0
_ipyw_jlab_nb_ext_conf 0.1.0 py38_0
alabaster 0.7.12 pyhd3eb1b0_0
anaconda custom py38_1
anaconda-client 1.7.2 py38_0
anaconda-navigator 2.0.3 py38_0
anaconda-project 0.9.1 pyhd3eb1b0_1
anndata 0.7.6 pypi_0 pypi anyio 2.2.0 py38hecd8cb5_1
applaunchservices 0.2.1 py_0
appnope 0.1.2 py38hecd8cb5_1001
appscript 1.1.2 py38h9ed2024_0
argh 0.26.2 py38_0
argon2-cffi 20.1.0 py38h9ed2024_1
asn1crypto 1.4.0 py_0
astroid 2.5 py38hecd8cb5_1
astropy 4.2.1 py38h9ed2024_1
async_generator 1.10 pyhd3eb1b0_0
atomicwrites 1.4.0 py_0
attrs 20.3.0 pyhd3eb1b0_0
autopep8 1.5.6 pyhd3eb1b0_0
babel 2.9.0 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
backports 1.0 pyhd3eb1b0_2
backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0
backports.shutil_get_terminal_size 1.0.0 pyhd3eb1b0_3
backports.tempfile 1.0 pyhd3eb1b0_1
backports.weakref 1.0.post1 py_1
beautifulsoup4 4.9.3 pyha847dfd_0
bitarray 1.9.2 py38h9ed2024_1
bkcharts 0.2 py38_0
blas 1.0 mkl
bleach 3.3.0 pyhd3eb1b0_0
blosc 1.21.0 h2842e9f_0
bokeh 2.3.1 py38hecd8cb5_0
boto 2.49.0 py38_0
bottleneck 1.3.2 py38hf1fa96c_1
brotlipy 0.7.0 py38h9ed2024_1003
bzip2 1.0.8 h1de35cc_0
c-ares 1.17.1 h9ed2024_0
ca-certificates 2021.4.13 hecd8cb5_1
certifi 2020.12.5 py38hecd8cb5_0
cffi 1.14.5 py38h2125817_0
chardet 4.0.0 py38hecd8cb5_1003
click 7.1.2 pyhd3eb1b0_0
cloudpickle 1.6.0 py_0
clyent 1.2.2 py38_1
colorama 0.4.4 pyhd3eb1b0_0
conda 4.10.1 py38hecd8cb5_1
conda-build 3.21.4 py38hecd8cb5_0
conda-content-trust 0.1.1 pyhd3eb1b0_0
conda-env 2.6.0 1
conda-package-handling 1.7.3 py38h9ed2024_1
conda-repo-cli 1.0.4 pyhd3eb1b0_0
conda-token 0.3.0 pyhd3eb1b0_0
conda-verify 3.4.2 py_1
contextlib2 0.6.0.post1 py_0
cryptography 3.4.7 py38h2fd3fbb_0
curl 7.71.1 hb0a8c7a_1
cycler 0.10.0 py38_0
cython 0.29.23 py38h23ab428_0
cytoolz 0.11.0 py38haf1e3a3_0
dask 2021.4.0 pyhd3eb1b0_0
dask-core 2021.4.0 pyhd3eb1b0_0
dbus 1.13.18 h18a8e69_0
decorator 4.4.2 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
diff-match-patch 20200713 py_0
distributed 2021.4.0 py38hecd8cb5_0
docutils 0.16 py38_1
entrypoints 0.3 py38_0
et_xmlfile 1.0.1 py_1001
expat 2.3.0 h23ab428_2
fastcache 1.1.0 py38h1de35cc_0
filelock 3.0.12 pyhd3eb1b0_1
flake8 3.9.0 pyhd3eb1b0_0
flask 1.1.2 pyhd3eb1b0_0
freetype 2.10.4 ha233b18_0
fsspec 0.9.0 pyhd3eb1b0_0
future 0.18.2 py38_1
get-version 2.2 pypi_0 pypi get_terminal_size 1.0.0 h7520d66_0
gettext 0.21.0 h7535e17_0
gevent 21.1.2 py38h9ed2024_1
glib 2.68.1 hdf23fa2_0
glob2 0.7 pyhd3eb1b0_0
gmp 6.2.1 h23ab428_2
gmpy2 2.0.8 py38h6ef4df4_3
greenlet 1.0.0 py38h23ab428_2
h5py 2.10.0 py38h3134771_0
hdf5 1.10.4 hfa1e0ec_0
heapdict 1.0.1 py_0
hnswlib 0.5.1 pypi_0 pypi html5lib 1.1 py_0
icu 58.2 h0a44026_3
idna 2.10 pyhd3eb1b0_0
imageio 2.9.0 pyhd3eb1b0_0
imagesize 1.2.0 pyhd3eb1b0_0
importlib-metadata 3.10.0 py38hecd8cb5_0
importlib_metadata 3.10.0 hd3eb1b0_0
iniconfig 1.1.1 pyhd3eb1b0_0
intel-openmp 2021.2.0 hecd8cb5_564
intervaltree 3.1.0 py_0
ipykernel 5.3.4 py38h5ca1d4c_0
ipython 7.22.0 py38h01d92e1_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.3 pyhd3eb1b0_1
isort 5.8.0 pyhd3eb1b0_0
itsdangerous 1.1.0 pyhd3eb1b0_0
jbig 2.1 h4d881f8_0
jdcal 1.4.1 py_0
jedi 0.17.1 py38_0
jinja2 2.11.3 pyhd3eb1b0_0
joblib 1.0.1 pyhd3eb1b0_0
jpeg 9b he5867d9_2
json5 0.9.5 py_0
jsonschema 3.2.0 py_2
jupyter 1.0.0 py38_7
jupyter-packaging 0.7.12 pyhd3eb1b0_0
jupyter_client 6.1.12 pyhd3eb1b0_0
jupyter_console 6.4.0 pyhd3eb1b0_0
jupyter_core 4.7.1 py38hecd8cb5_0
jupyter_server 1.4.1 py38hecd8cb5_0
jupyterlab 3.0.14 pyhd3eb1b0_1
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.4.0 pyhd3eb1b0_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
keyring 22.3.0 py38hecd8cb5_0
kiwisolver 1.3.1 py38h23ab428_0
krb5 1.18.2 h75d18d8_0
lazy-object-proxy 1.6.0 py38h9ed2024_0
lcms2 2.12 hf1fd2bf_0
legacy-api-wrap 1.2 pypi_0 pypi libarchive 3.4.2 haa3ed63_0
libcurl 7.71.1 h8a08a2b_1
libcxx 10.0.0 1
libedit 3.1.20210216 h9ed2024_1
libev 4.33 haf1e3a3_0
libffi 3.3 hb1e8313_2
libgfortran 3.0.1 h93005f0_2
libiconv 1.16 h1de35cc_0
liblief 0.10.1 h0a44026_0
libllvm10 10.0.1 h76017ad_5
libllvm9 9.0.1 h21ff451_1
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 h1de35cc_0
libspatialindex 1.9.3 h23ab428_0
libssh2 1.9.0 ha12b0ac_1
libtiff 4.2.0 h87d7836_0
libuv 1.40.0 haf1e3a3_0
libwebp-base 1.2.0 h9ed2024_0
libxml2 2.9.10 h7cdb67c_3
libxslt 1.1.34 h83b36ba_0
llvm-openmp 10.0.0 h28b9765_0
llvmlite 0.34.0 py38h739e7dc_4
locket 0.2.1 py38hecd8cb5_1
loompy 3.0.6 pypi_0 pypi louvain 0.7.0 pypi_0 pypi lxml 4.6.3 py38h26b266a_0
lz4-c 1.9.3 h23ab428_0
lzo 2.10 haf1e3a3_2
markupsafe 1.1.1 py38h1de35cc_1
matplotlib 3.3.4 py38hecd8cb5_0
matplotlib-base 3.3.4 py38h8b3ea08_0
mccabe 0.6.1 py38_1
mistune 0.8.4 py38h1de35cc_1001
mkl 2021.2.0 hecd8cb5_269
mkl-service 2.3.0 py38h9ed2024_1
mkl_fft 1.3.0 py38h4a7008c_2
mkl_random 1.2.1 py38hb2f4e1b_2
mock 4.0.3 pyhd3eb1b0_0
more-itertools 8.7.0 pyhd3eb1b0_0
mpc 1.1.0 h6ef4df4_1
mpfr 4.0.2 h9066e36_1
mpmath 1.2.1 py38hecd8cb5_0
msgpack-python 1.0.2 py38hf7b0b51_1
multipledispatch 0.6.0 py38_0
natsort 7.1.1 pypi_0 pypi navigator-updater 0.2.1 py38_0
nbclassic 0.2.6 pyhd3eb1b0_0
nbclient 0.5.3 pyhd3eb1b0_0
nbconvert 6.0.7 py38_0
nbformat 5.1.3 pyhd3eb1b0_0
ncurses 6.2 h0a44026_1
nest-asyncio 1.5.1 pyhd3eb1b0_0
networkx 2.5.1 pyhd3eb1b0_0
nltk 3.6.1 pyhd3eb1b0_0
nose 1.3.7 pyhd3eb1b0_1006
notebook 6.3.0 py38hecd8cb5_0
numba 0.51.2 py38h6440ff4_1
numexpr 2.7.3 py38h5873af2_1
numpy 1.20.1 py38hd6e1bb9_0
numpy-base 1.20.1 py38h585ceec_0
numpy-groupies 0.9.13 pypi_0 pypi numpydoc 1.1.0 pyhd3eb1b0_1
olefile 0.46 py_0
openpyxl 3.0.7 pyhd3eb1b0_0
openssl 1.1.1k h9ed2024_0
packaging 20.9 pyhd3eb1b0_0
pandas 1.2.4 py38h23ab428_0
pandoc 2.12 hecd8cb5_0
pandocfilters 1.4.3 py38hecd8cb5_1
parso 0.7.0 py_0
partd 1.2.0 pyhd3eb1b0_0
path 15.1.2 py38hecd8cb5_0
path.py 12.5.0 0
pathlib2 2.3.5 py38hecd8cb5_2
pathtools 0.1.2 py_1
patsy 0.5.1 py38_0
pcre 8.44 hb1e8313_0
pep8 1.7.1 py38_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 8.2.0 py38h5270095_0
pip 21.0.1 py38hecd8cb5_0
pkginfo 1.7.0 py38hecd8cb5_0
pluggy 0.13.1 py38hecd8cb5_0
ply 3.11 py38_0
prometheus_client 0.10.1 pyhd3eb1b0_0
prompt-toolkit 3.0.17 pyh06a4308_0
prompt_toolkit 3.0.17 hd3eb1b0_0
psutil 5.8.0 py38h9ed2024_1
ptyprocess 0.7.0 pyhd3eb1b0_2
py 1.10.0 pyhd3eb1b0_0
py-lief 0.10.1 py38haf313ee_0
pybind11 2.6.2 pypi_0 pypi pycodestyle 2.6.0 pyhd3eb1b0_0
pycosat 0.6.3 py38h1de35cc_1
pycparser 2.20 py_2
pycurl 7.43.0.6 py38hddc9c9b_0
pydocstyle 6.0.0 pyhd3eb1b0_0
pyerfa 1.7.3 py38h9ed2024_0
pyflakes 2.2.0 pyhd3eb1b0_0
pygments 2.8.1 pyhd3eb1b0_0
pylint 2.7.4 py38hecd8cb5_1
pyodbc 4.0.30 py38h0a44026_0
pyopenssl 20.0.1 pyhd3eb1b0_1
pyparsing 2.4.7 pyhd3eb1b0_0
pyqt 5.9.2 py38h655552a_2
pyrsistent 0.17.3 py38haf1e3a3_0
pysam 0.16.0.1 pypi_0 pypi pysocks 1.7.1 py38_1
pytables 3.6.1 py38h4727e94_0
pytest 6.2.3 py38hecd8cb5_2
python 3.8.8 h88f2d9e_5
python-dateutil 2.8.1 pyhd3eb1b0_0
python-igraph 0.9.1 pypi_0 pypi python-jsonrpc-server 0.4.0 py_0
python-language-server 0.35.1 py_0
python-libarchive-c 2.9 pyhd3eb1b0_1
python.app 3 py38h9ed2024_0
pytz 2021.1 pyhd3eb1b0_0
pywavelets 1.1.1 py38haf1e3a3_2
pyyaml 5.4.1 py38h9ed2024_1
pyzmq 20.0.0 py38h23ab428_1
qdarkstyle 3.0.2 pyhd3eb1b0_0
qt 5.9.7 h468cd18_1
qtawesome 1.0.2 pyhd3eb1b0_0
qtconsole 5.0.3 pyhd3eb1b0_0
qtpy 1.9.0 py_0
readline 8.1 h9ed2024_0
regex 2021.4.4 py38h9ed2024_0
requests 2.25.1 pyhd3eb1b0_0
ripgrep 12.1.1 0
rope 0.18.0 py_0
rtree 0.9.7 py38hecd8cb5_1
ruamel_yaml 0.15.100 py38h9ed2024_0
samtools 1.4.1 0 bioconda scanpy 1.7.2 pypi_0 pypi scikit-image 0.18.1 py38hb2f4e1b_0
scikit-learn 0.24.1 py38hb2f4e1b_0
scipy 1.6.2 py38hd5f7400_1
scvelo 0.2.3 pypi_0 pypi seaborn 0.11.1 pyhd3eb1b0_0
send2trash 1.5.0 pyhd3eb1b0_1
setuptools 52.0.0 py38hecd8cb5_0
simplegeneric 0.8.1 py38_2
sinfo 0.3.4 pypi_0 pypi singledispatch 3.6.1 pyhd3eb1b0_1001
sip 4.19.8 py38h0a44026_0
six 1.15.0 py38hecd8cb5_0
snappy 1.1.8 hb1e8313_0
sniffio 1.2.0 py38hecd8cb5_1
snowballstemmer 2.1.0 pyhd3eb1b0_0
sortedcollections 2.1.0 pyhd3eb1b0_0
sortedcontainers 2.3.0 pyhd3eb1b0_0
soupsieve 2.2.1 pyhd3eb1b0_0
sphinx 3.5.4 pyhd3eb1b0_0
sphinxcontrib 1.0 py38_1
sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-htmlhelp 1.0.3 pyhd3eb1b0_0
sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0
sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.4 pyhd3eb1b0_0
sphinxcontrib-websupport 1.2.4 py_0
spyder 4.1.5 py38_0
spyder-kernels 1.9.4 py38_0
sqlalchemy 1.4.7 py38h9ed2024_0
sqlite 3.35.4 hce871da_0
statsmodels 0.12.2 py38h9ed2024_0
stdlib-list 0.8.0 pypi_0 pypi sympy 1.8 py38hecd8cb5_0
tbb 2021.2.0 hf7b0b51_0
tblib 1.7.0 py_0
terminado 0.9.4 py38hecd8cb5_0
testpath 0.4.4 pyhd3eb1b0_0
texttable 1.6.3 pypi_0 pypi threadpoolctl 2.1.0 pyh5ca1d4c_0
tifffile 2020.10.1 py38h0cf3a3e_2
tk 8.6.10 hb0a8c7a_0
toml 0.10.2 pyhd3eb1b0_0
toolz 0.11.1 pyhd3eb1b0_0
tornado 6.1 py38h9ed2024_0
tqdm 4.59.0 pyhd3eb1b0_1
traitlets 5.0.5 pyhd3eb1b0_0
typing_extensions 3.7.4.3 pyha847dfd_0
ujson 4.0.2 py38h23ab428_0
umap-learn 0.4.6 pypi_0 pypi unicodecsv 0.14.1 py38_0
unixodbc 2.3.9 haf1e3a3_0
urllib3 1.26.4 pyhd3eb1b0_0
velocyto 0.17.17 pypi_0 pypi watchdog 1.0.2 py38h9ed2024_1
wcwidth 0.2.5 py_0
webencodings 0.5.1 py38_1
werkzeug 1.0.1 pyhd3eb1b0_0
wheel 0.36.2 pyhd3eb1b0_0
widgetsnbextension 3.5.1 py38_0
wrapt 1.12.1 py38haf1e3a3_1
wurlitzer 2.1.0 py38hecd8cb5_0
xlrd 2.0.1 pyhd3eb1b0_0
xlsxwriter 1.3.8 pyhd3eb1b0_0
xlwings 0.23.0 py38hecd8cb5_0
xlwt 1.3.0 py38_0
xmltodict 0.12.0 py_0
xz 5.2.5 h1de35cc_0
yaml 0.2.5 haf1e3a3_0
yapf 0.31.0 pyhd3eb1b0_0
zeromq 4.3.4 h23ab428_0
zict 2.0.0 pyhd3eb1b0_0
zipp 3.4.1 pyhd3eb1b0_0
zlib 1.2.11 h1de35cc_3
zope 1.0 py38_1
zope.event 4.5.0 py38_0
zope.interface 5.3.0 py38h9ed2024_0
zstd 1.4.5 h41d2c2f_0

Thanks a lot in advance for your help,

egeulgen commented 3 years ago

hey @cguetta,

please create an issue on velocyto's github repository: https://github.com/velocyto-team/velocyto.R

cguetta commented 3 years ago

Hello,

Thanks a lot for your answer.

I am new to github and I did not realize that I created the issue at the wrong place. I am sorry about that. I now created it in the velocyto (or at least I hope that I did it correctly this time).

Thanks a lot in advance for your help,

Best regards,

Charlotte

From: Ege Ulgen @.> Reply-To: egeulgen/pathfindR @.> Date: Tuesday, May 11, 2021 at 17:38 To: egeulgen/pathfindR @.> Cc: cguetta @.>, Mention @.***> Subject: Re: [egeulgen/pathfindR] Problem with samtools : dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib (#78)

hey @cguettahttps://github.com/cguetta,

please create an issue on velocyto's github repository: https://github.com/velocyto-team/velocyto.R

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/egeulgen/pathfindR/issues/78#issuecomment-839194898, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUBEVT4RUV5K3QVK2DSFEBDTNGPUFANCNFSM44WJN6PA.