Issues

• (BCB430 #31) Document external files the build needs that can't be in the repo

  BaderLab/EnrichmentMap_monthlyGenesetBuild#53 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #30) Remove the jar rebuild from docker-entrypoint.sh

  BaderLab/EnrichmentMap_monthlyGenesetBuild#52 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #29) SSL certificate verification disabled in Geneset_tracking.Rmd

  BaderLab/EnrichmentMap_monthlyGenesetBuild#51 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #28) Drug, miR and Disease figures never shown in the summary report

  BaderLab/EnrichmentMap_monthlyGenesetBuild#50 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #27) ggplots inside if blocks are saved as blank PNGs

  BaderLab/EnrichmentMap_monthlyGenesetBuild#49 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #26) miR and Disease/Phenotype figures never drawn (inverted NULL check)

  BaderLab/EnrichmentMap_monthlyGenesetBuild#48 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #25) Stats table never initialised if newest release has no summary file

  BaderLab/EnrichmentMap_monthlyGenesetBuild#47 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #24) Geneset_tracking.Rmd continues with no data when download site is unreachable

  BaderLab/EnrichmentMap_monthlyGenesetBuild#46 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #23) Failed log download not detected in Geneset_tracking.Rmd

  BaderLab/EnrichmentMap_monthlyGenesetBuild#45 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #22) Geneset_tracking.Rmd crashes on R 4.3+ ("||" used with a vector)

  BaderLab/EnrichmentMap_monthlyGenesetBuild#44 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #21) Slack always posts "Finished" regardless of build outcome

  BaderLab/EnrichmentMap_monthlyGenesetBuild#43 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #20) Summary README replaced even when the R report fails

  BaderLab/EnrichmentMap_monthlyGenesetBuild#42 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #19) Taxid filter commented out for Gene_Name/GeneID UniProt lookups

  BaderLab/EnrichmentMap_monthlyGenesetBuild#41 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #18) GenesetTools exits with status 0 on bad arguments or failed GMT load

  BaderLab/EnrichmentMap_monthlyGenesetBuild#40 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #17) UniProt web service errors are swallowed and GMT written with partial results

  BaderLab/EnrichmentMap_monthlyGenesetBuild#39 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #16) UniProt ID batching skips one ID per 1000 and drops the last ID

  BaderLab/EnrichmentMap_monthlyGenesetBuild#38 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #15) UniProt job status check can loop forever (attempt = attempt++)

  BaderLab/EnrichmentMap_monthlyGenesetBuild#37 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #14) Remove hard-coded BioCyc and DrugBank credentials from scripts

  BaderLab/EnrichmentMap_monthlyGenesetBuild#36 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #13) Rat build still downloads go.obo over http LABELS: bug, good first issue

  BaderLab/EnrichmentMap_monthlyGenesetBuild#35 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #12) Empty GMT files created when BioPAX parsing fails

  BaderLab/EnrichmentMap_monthlyGenesetBuild#34 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #11) Version info not saved for HumanCyc, NCI and NetPath static sources

  BaderLab/EnrichmentMap_monthlyGenesetBuild#33 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #10) Rat Reactome doesn't pass taxid, so species check is skipped

  BaderLab/EnrichmentMap_monthlyGenesetBuild#32 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #9) Woodchuck translation summary never created (checks for mouse taxid 10090)

  BaderLab/EnrichmentMap_monthlyGenesetBuild#31 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #8) "Huamn" typo in published Woodchuck GMT file name

  BaderLab/EnrichmentMap_monthlyGenesetBuild#30 · Filter by author rmobmina opened on Oct 29, 2026

• (BCB430 #7) Comment missing "#" causes "create: command not found" in every build log

  BaderLab/EnrichmentMap_monthlyGenesetBuild#29 · Filter by author rmobmina opened on Oct 29, 2026