# Generate Heatmaps Failing

## Tags

* type: bug
* status: open
* priority: medium
* assigned: fredm, zachs, zsloan
* keywords: genenetwork3, gn3, GN3, heatmaps

## Reproduce

* Go to https://genenetwork.org/
* Under "Select and Search" menu, enter "synap*" for the "Get Any" field
* Click "Search"
* In search results page, select first 10 traits
* Click "Add"
* Under "Create a new collection" enter the name "newcoll" and click "Create collection"
* In the collections page that shows up, click "Select All" once
* Ensure all the traits are selected
* Click "Generate Heatmap" and wait
* Note how system fails silently with no heatmap presented

### Notes

On https://gn2-fred.genenetwork.org the heatmaps fails with a note ("ERROR: undefined"). In the logs, I see "Module 'scipy' has no attribute 'array'" which seems to be due to a change in numpy.
=> https://github.com/MaartenGr/BERTopic/issues/1791
=> https://github.com/scipy/scipy/issues/19972

This issue should not be present with python-plotly@5.20.0 but since guix-bioinformatics pins the guix version to `b0b988c41c9e0e591274495a1b2d6f27fcdae15a`, we are not able to pull in newer versions of packages from guix.


### Update 2025-04-08T10:59CDT

Got the following error when I ran the background command manually:

```
$ export RUST_BACKTRACE=full
$ /gnu/store/dp4zq4xiap6rp7h6vslwl1n52bd8gnwm-profile/bin/qtlreaper --geno /home/frederick/genotype_files/genotype/genotype/BXD.geno --n_permutations 1000 --traits /tmp/traits_test_file_n2E7V06Cx7.txt --main_output /tmp/qtlreaper/main_output_NGVW4sfYha.txt --permu_output /tmp/qtlreaper/permu_output_MJnzLbrsrC.txt
thread 'main' panicked at src/regression.rs:216:25:
index out of bounds: the len is 20 but the index is 20
stack backtrace:
   0:     0x61399d77d46d - <unknown>
   1:     0x61399d7b5e13 - <unknown>
   2:     0x61399d78b649 - <unknown>
   3:     0x61399d78f26f - <unknown>
   4:     0x61399d78ee98 - <unknown>
   5:     0x61399d78f815 - <unknown>
   6:     0x61399d77d859 - <unknown>
   7:     0x61399d77d679 - <unknown>
   8:     0x61399d78f3f4 - <unknown>
   9:     0x61399d6f4063 - <unknown>
  10:     0x61399d6f41f7 - <unknown>
  11:     0x61399d708f18 - <unknown>
  12:     0x61399d6f6e4e - <unknown>
  13:     0x61399d6f9e93 - <unknown>
  14:     0x61399d6f9e89 - <unknown>
  15:     0x61399d78e505 - <unknown>
  16:     0x61399d6f8d55 - <unknown>
  17:     0x75ee2b945bf7 - __libc_start_call_main
  18:     0x75ee2b945cac - __libc_start_main@GLIBC_2.2.5
  19:     0x61399d6f4861 - <unknown>
  20:                0x0 - <unknown>
```