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IGS / FADU

Feature Aggregate Depth Utility
GNU Affero General Public License v3.0
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CHOLMOD version incompatibility? #15

Closed Niohuruzh closed 3 weeks ago

Niohuruzh commented 3 weeks ago

Hi Is there any problem when CHOLMOD version incompatibility?

┌ Warning: CHOLMOD version incompatibility │ │ Julia was compiled with CHOLMOD version 4.0.4. It is │ currently linked with version 5.3.0. │ This might cause Julia to terminate when working with │ sparse matrix factorizations, e.g. solving systems of │ equations with \. │ │ It is recommended that you use Julia with the same major │ version of CHOLMOD as the one used during the build, or │ download the generic binaries from www.julialang.org, │ which ship with the correct versions of all dependencies. └ @ SparseArrays.CHOLMOD ~/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:206

And there is little different result compared to Example command result. Here is my result:

featureID uniq_len num_alignments counts tpm cds0 1017 4.5 2.81 1755.54 cds1 1194 3.5 2.48 1318.88

adkinsrs commented 3 weeks ago

@Niohuruzh, how was your version of Julia installed? Did you perform the installation or was this done by a sysadmin?

It seems like only the TPM values between your example and the documentation example are slightly off. I did some research, and CHOLMOD seems to be a SparseArrays-related module file which FADU does not use, at least not directly. Can you paste your package versions (open the REPL, hit "]", then type in "status" and hit Enter). I personally do not have the SparseArrays.jl packagin installed.

Niohuruzh commented 3 weeks ago

Hi, Thanks for your reply. Julia(Version 1.10.3) is installed by conda.

[c7e460c6] ArgParse v1.2.0 [8e4a8c10] BED v0.3.0 [28d598bf] BGZFStreams v0.3.2 [af1dc308] GFF3 v0.2.3 [899a7d2d] GenomicFeatures v2.1.0 [4ffb77ac] Indexes v0.1.3 [09ab397b] StructArrays v0.6.18 [d759349c] XAM v0.3.1 [56ddb016] Logging

adkinsrs commented 3 weeks ago

Thanks.

I have not actually tried FADU in Julia 1.10+ yet. Most recent version I have tested is 1.9.

I went ahead and re-ran FADU with the packages I have and noticed that I get identical TPMs as you. The last time I updated that table in the README was apparently 6 years ago (and 2 years before we put out the paper)! So I think I need to update the table in the README, since there were developments that would have changed the calculations slightly

Niohuruzh commented 3 weeks ago

Thank you! It seems that my installed FADU is working correctly.