cutpatel
commented
2 years ago Is no one else habing this problem? For me exactly this happend with the Statistics::R module. Had to manually move the module one level up. Then it was in @INC again and worked. Any other ideas?
conda --version
conda 4.11.0
conda list
# packages in environment at /*/miniconda3/envs/resreport:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310h6acc77f_1 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_4 conda-forge
black 22.1.0 pyhd8ed1ab_0 conda-forge
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.5.18.1 ha878542_0 conda-forge
cairo 1.16.0 ha00ac49_1009 conda-forge
cffi 1.15.0 py310h0fdd8cc_0 conda-forge
click 8.0.3 py310hff52083_1 conda-forge
curl 7.81.0 h494985f_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
debugpy 1.5.1 py310h122e73d_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
executing 0.8.2 pyhd8ed1ab_0 conda-forge
flit-core 3.6.0 pyhd8ed1ab_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 2.13.94 ha180cfb_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc 9.4.0 h192d537_10 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_12 conda-forge
gcc_linux-64 9.4.0 h391b98a_4 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_12 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_4 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_12 conda-forge
gxx_linux-64 9.4.0 h0316aca_4 conda-forge
harfbuzz 3.3.1 hb4a5f5f_0 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
importlib-metadata 4.10.1 py310hff52083_0 conda-forge
importlib_resources 5.4.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.8.0 py310hfdc917e_0 conda-forge
ipython 8.0.1 py310hff52083_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.1 py310hff52083_0 conda-forge
jinja2 3.0.3 pyhd8ed1ab_0 conda-forge
jpeg 9e h7f98852_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.1.2 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.1 py310hff52083_1 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
krb5 1.19.2 h48eae69_3 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.81.0 h494985f_0 conda-forge
libdeflate 1.8 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_12 conda-forge
libgcc-ng 11.2.0 h1d223b6_12 conda-forge
libgfortran-ng 11.2.0 h69a702a_12 conda-forge
libgfortran5 11.2.0 h5c6108e_12 conda-forge
libglib 2.70.2 h174f98d_1 conda-forge
libgomp 11.2.0 h1d223b6_12 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnghttp2 1.46.0 ha19adfc_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsanitizer 9.4.0 h79bfe98_12 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_12 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_12 conda-forge
libtiff 4.3.0 h6f004c6_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
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make 4.3 hd18ef5c_1 conda-forge
markupsafe 2.0.1 py310h6acc77f_1 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
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nbclient 0.5.10 pyhd8ed1ab_1 conda-forge
nbconvert 6.4.1 py310hff52083_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
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nest-asyncio 1.5.4 pyhd8ed1ab_0 conda-forge
notebook 6.4.8 pyha770c72_0 conda-forge
openssl 3.0.3 h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandoc 2.17.1.1 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.48.10 h54213e6_2 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
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pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
perl 5.32.1 1_h7f98852_perl5 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge
perl-getopt-long 2.50 pl5321hdfd78af_2 bioconda
perl-io-tty 1.16 pl5321hec16e2b_1 bioconda
perl-ipc-run 20200505.0 pl5321hdfd78af_0 bioconda
perl-regexp-common 2017060201 pl5321hdfd78af_1 bioconda
perl-statistics-r 0.34 0 bioconda
perl-text-balanced 2.05 pl5321hdfd78af_0 bioconda
perl-text-wrap 2021.0814 pl5321hdfd78af_0 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-vars 1.03 pl5321hdfd78af_2 bioconda
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pip 22.0.2 pyhd8ed1ab_1 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
platformdirs 2.3.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.13.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.26 pyha770c72_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
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pyrsistent 0.18.1 py310h6acc77f_0 conda-forge
python 3.10.2 hc74c709_3_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
pyzmq 22.3.0 py310h675a958_1 conda-forge
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wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.1 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-libxt 1.2.1 h7f98852_2 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
xz 5.2.5 h516909a_1 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
There is a number of perl modules on bioconda that get installed outside the paths visible to perl, i.e. outside the
@INCvariable thus leading to a broken environment.Here's an example to reproduce the issue - these are modules from the recipe for meme:
This completes ok but then I get:
There reason is that the XML module was installed in
$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/XML/Simple.pm. Adding$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/toPERL5LIBdoes not help:I think this issue has been observed before (e.g. #20459) - I don't know if there is a general fix?
These are my settings: