1 files changed, 51 insertions, 3 deletions

diff --git a/issues/fix-broken-builds-in-gn2-and-gn3.gmi b/issues/fix-broken-builds-in-gn2-and-gn3.gmi
index cf9506f..3c0e6aa 100644
--- a/issues/fix-broken-builds-in-gn2-and-gn3.gmi
+++ b/issues/fix-broken-builds-in-gn2-and-gn3.gmi
@@ -5,7 +5,55 @@ gn3 and gn2.
 
 ## Tasks
 
-* assigned: bonfacekilz
+* assigned: bonfacekilz, efraim
 
-* [ ] Fix pylint/ mypy issues in gn3
-* [ ] Update docker image in gn2
+### Notes
+
+At the moment, we are getting the following build failures in gn2,
+
+```
+Compiling '/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/wqflask/wgcna/wgcna_analysis.py'...
+Compiling '/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/wsgi.py'...
+error: in phase 'install': uncaught exception:
+%exception #<&invoke-error program: "python" arguments: ("-m" "compileall" "--invalidation-mode=unchecked-hash" "/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9") exit-status: 1 term-signal: #f stop-signal: #f> 
+phase `install' failed after 0.9 seconds
+command "python" "-m" "compileall" "--invalidation-mode=unchecked-hash" "/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9" failed with status 1
+note: keeping build directory `/tmp/guix-build-genenetwork2-3.11-guix-fe345c9.drv-0'
+builder for `/gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv' failed with exit code 1
+build of /gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv failed
+View build log at '/var/log/guix/drvs/l5/hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv.bz2'.
+guix build: error: build of `/gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv' failed
+
+```
+
+Some missing bits from the build log:
+
+```
+Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/redis_tools.py'...
+Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/startup_config.py'...
+Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/svg.py'...
+***   File "/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/svg.py", line 113
+    True = 1
+        ^
+        SyntaxError: cannot assign to True
+
+Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/temp_data.py'...
+Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/tools.py'...
+
+```
+
+This starts happening (not yet comfirmed) when python is bumped up
+from 3.8 to 3.9
+
+In addition, there are some dependencies of genenetwork2 which FTBFS, due to incorrect versions of inputs.
+
+```
+ starting phase `sanity-check'¬
+ validating 'pingouin' /gnu/store/dpy5ln4zjgv53l8jpm1qalwn45cagxfm-python-pingouin-0.5.0/lib/python3.9/site-packages¬
+ ...checking requirements: ERROR: pingouin==0.5.0 (statsmodels 0.11.1 (/gnu/store/ab8k9bwmaml2bplq4bd9xkg08z7bn8fr-python-statsmodels-0.11.1/lib/python3.9/site-packages), Requirement.parse('statsmodels>=0.12.0'), {'pingouin'})¬
+ error: in phase 'sanity-check': uncaught exception:¬
+ %exception #<&invoke-error program: "python" arguments: ("/gnu/store/nwwr89v2vyg1hs48i49m083vhczsgh3m-sanity-check.py" "/gnu/store/dpy5ln4zjgv53l8jpm1qalwn45cagxfm-python-pingouin-0.5.0/lib/python3.9/site-packages") exit-status: 1 term-signal: #f stop-signal: #f>▸¬
+ phase `sanity-check' failed after 0.1 seconds¬
+```
+
+This was fixed by reverting the update to python-pingouin, dropping it back to 0.3.12.