error when installing via conda
Closed this issue · 2 comments
Jane-Gibson commented
I have installed via conda as described but get the following error when trying to run it, even just to get the help screen:
(conda_env)[jg]$ modbam2bed --help
modbam2bed: symbol lookup error: modbam2bed: undefined symbol: bam_mods_at_qpos
Any help appreciated.
Thanks, Jane
cjw85 commented
Hi @Jane-Gibson,
Can you confirm you installed modbam2bed in a clean conda environment? I suspect what has happened here is that you have it installed in an environment with an older version of the htslib package than is required. I cannot reproduce your error when installing into a new environment.
When I install the program in a new environment and run conda list I see:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
htslib 1.15.1 h9753748_0 bioconda
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_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
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libzlib 1.2.12 h166bdaf_1 conda-forge
modbam2bed 0.6.2 h9bf148f_0 epi2melabs
ncurses 6.3 h27087fc_1 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.12 h166bdaf_1 conda-forge
Jane-Gibson commented
Yes that was it, sorry.
All working now in new env.