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sequence-formats-1.12.1.0

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Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
67/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Active
Tech stack
haskell
Domain
build-system

Research direction

The failure is in src-executables/vcf2eigenstrat.hs at line 110 while building sequenceTools. Start by reading the code around the vcfToFreqSumEntry call and checking its return type against the value passed to yield. Run the reported Stack build to verify the error is resolved; the issue gives no test-file path.

Written by the indexing model from the issue text.

Description

failure: compile

@stschiff

Error: [S-7282]
       Stack failed to execute the build plan.

       While executing the build plan, Stack encountered the error:

       [S-7011]
       While building package sequenceTools-1.6.0.0 (scroll up to its section to see the error) using:
       /home/curators/.stack/setup-exe-cache/x86_64-linux-tinfo6/Cabal-simple_w2MFVN35_3.14.2.0_ghc-9.12.4 --verbose=1 --builddir=.stack-work/dist/x86_64-linux-tinfo6/ghc-9.12.4 build lib:sequenceTools exe:genoStats exe:pileupCaller exe:vcf2eigenstrat test:sequenceToolsTests --ghc-options " -fdiagnostics-color=always"
       Process exited with code: ExitFailure 1
       Logs have been written to: /home/curators/work/unpack-dir/.stack-work/logs/sequenceTools-1.6.0.0.log

       Preprocessing library for sequenceTools-1.6.0.0...
       Building library for sequenceTools-1.6.0.0...
       Preprocessing executable 'vcf2eigenstrat' for sequenceTools-1.6.0.0...
       Building executable 'vcf2eigenstrat' for sequenceTools-1.6.0.0...
       [1 of 1] Compiling Main
       /home/curators/work/unpack-dir/unpacked/sequenceTools-1.6.0.0-9efb7f266292a58a990b571d03513b835b54d2844d0964bb1571e00b9ba90a4a/src-executables/vcf2eigenstrat.hs:110:11: error: [GHC-83865]
           • Couldn't match expected type ‘FreqSumEntry’
                         with actual type ‘Maybe FreqSumEntry’
           • In the first argument of ‘yield’, namely ‘fs’
             In a stmt of a 'do' block: yield fs
             In the expression:
               do fs <- liftIO $ vcfToFreqSumEntry e
                  yield fs
           |
       110 |     yield fs
           |           ^^
curator: Received ExitFailure 1 when running
Raw command: /usr/bin/stack --terminal build --test --test-suite-timeout=600 --no-rerun-tests --bench --no-run-benchmarks --haddock --no-interleaved-output --ghc-options -w --jobs=16
Run from: unpack-dir
Dominant language
Dockerfile
Stars
550
Forks
827
Avg merge
23h 15m
Merged PRs (30d)
7

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