4 files changed, 122 insertions, 0 deletions

diff --git a/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip b/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip
new file mode 100644
index 0000000..7681b88
--- /dev/null
+++ b/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip
diff --git a/issues/genenetwork3/ctl-maps-error.gmi b/issues/genenetwork3/ctl-maps-error.gmi
new file mode 100644
index 0000000..6726357
--- /dev/null
+++ b/issues/genenetwork3/ctl-maps-error.gmi
@@ -0,0 +1,46 @@
+# CTL Maps Error
+
+## Tags
+
+* type: bug
+* status: open
+* priority: high
+* assigned: alexm, zachs, fredm
+* keywords: CTL, CTL Maps, gn3, genetwork3, genenetwork 3
+
+## Description
+
+Trying to run the CTL Maps feature in the collections page as described in
+=> /issues/genenetwork2/broken-collections-feature
+
+We get an error in the results page of the form:
+
+```
+{'error': '{\'code\': 1, \'output\': \'Loading required package: MASS\\nLoading required package: parallel\\nLoading required package: qtl\\nThere were 13 warnings (use warnings() to see them)\\nError in xspline(x, y, shape = 0, lwd = lwd, border = col, lty = lty, : \\n invalid value specified for graphical parameter "lwd"\\nCalls: ctl.lineplot -> draw.spline -> xspline\\nExecution halted\\n\'}'}
+```
+
+on the CLI the same error is rendered:
+```
+Loading required package: MASS
+Loading required package: parallel
+Loading required package: qtl
+There were 13 warnings (use warnings() to see them)
+Error in xspline(x, y, shape = 0, lwd = lwd, border = col, lty = lty,  : 
+  invalid value specified for graphical parameter "lwd"
+Calls: ctl.lineplot -> draw.spline -> xspline
+Execution halted
+```
+
+On my local development machine, the command run was
+```
+Rscript /home/frederick/genenetwork/genenetwork3/scripts/ctl_analysis.R /tmp/01828928-26e6-4cad-bbc8-59fd7a7977de.json
+```
+
+Here is a zipped version of the json file (follow the link and click download):
+=> https://github.com/genenetwork/gn-gemtext-threads/blob/main/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip
+
+Troubleshooting a while, I suspect
+=> https://github.com/genenetwork/genenetwork3/blob/27d9c9d6ef7f37066fc63af3d6585bf18aeec925/scripts/ctl_analysis.R#L79-L80 this is the offending code.
+
+=> https://cran.r-project.org/web/packages/ctl/ctl.pdf The manual for the ctl library
+indicates that our call above might be okay, which might mean something changed in the dependencies that the ctl library used.
diff --git a/issues/genenetwork3/generate-heatmaps-failing.gmi b/issues/genenetwork3/generate-heatmaps-failing.gmi
index 03256e6..522dc27 100644
--- a/issues/genenetwork3/generate-heatmaps-failing.gmi
+++ b/issues/genenetwork3/generate-heatmaps-failing.gmi
@@ -28,3 +28,37 @@ On https://gn2-fred.genenetwork.org the heatmaps fails with a note ("ERROR: unde
 => 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>
+```
diff --git a/issues/genenetwork3/rqtl2-mapping-error.gmi b/issues/genenetwork3/rqtl2-mapping-error.gmi
new file mode 100644
index 0000000..480c7c6
--- /dev/null
+++ b/issues/genenetwork3/rqtl2-mapping-error.gmi
@@ -0,0 +1,42 @@
+# R/qtl2 Maps Error
+
+## Tags
+
+* type: bug
+* status: open
+* priority: high
+* assigned: alexm, zachs, fredm
+* keywords: R/qtl2, R/qtl2 Maps, gn3, genetwork3, genenetwork 3
+
+## Reproduce
+
+* Go to https://genenetwork.org/
+* In the "Get Any" field, enter "synap*" and press the "Enter" key
+* In the search results, click on the "1435464_at" trait
+* Expand the "Mapping Tools" accordion section
+* Select the "R/qtl2" option
+* Click "Compute"
+* In the "Computing the Maps" page that results, click on "Display System Log"
+
+### Observed
+
+A traceback is observed, with an error of the following form:
+
+```
+⋮
+FileNotFoundError: [Errno 2] No such file or directory: '/opt/gn/tmp/gn3-tmpdir/JL9PvKm3OyKk.txt'
+```
+
+### Expected
+
+The mapping runs successfully and the results are presented in the form of a mapping chart/graph and a table of values.
+
+### Debug Notes
+
+The directory "/opt/gn/tmp/gn3-tmpdir/" exists, and is actually used by other mappings (i.e. The "R/qtl" and "Pair Scan" mappings) successfully.
+
+This might imply a code issue: Perhaps
+* a path is hardcoded, or
+* the wrong path value is passed
+
+The same error occurs on https://cd.genenetwork.org but does not seem to prevent CD from running the mapping to completion. Maybe something is missing on production — what, though?