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funpopgen / CaVEMaN

Causal Variant Evidence Mapping with Non-parametric resampling
https://funpopgen.github.io/CaVEMaN/
GNU General Public License v3.0
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src/run_analysis.d(3): Error #2

Open XscapeCn opened 3 years ago

XscapeCn commented 3 years ago

I'm sorry to bother you, but I still get the following error after repeated attempts.

Environments: ldc: 2-1.24.0 dmd: 2.094.2 gsl: 2.6

/data1/home/songxu/software/ldc2-1.24.0-linux-x86_64/bin/ldc2 -Jviews -d-debug -g -unittest -w src/arg_parse.d src/run_analysis.d src/correct.d src/best.d src/weights.d src/calculation.d src/main.d src/read_data.d src/interpolate.o -ofunittest src/run_analysis.d(3): Error: module calculation member Opts is not visible from module run_analysis make: *** [test] Error 1

Please advice.

abrown25 commented 3 years ago

Apologies, compiler moved on but the code didn't. Just pushed change that will allow it to compile if you pull master

XscapeCn commented 3 years ago

Thank you But I got another wrong 

cc    -c -o src/interpolate.o src/interpolate.c
/data1/home/songxu/software/ldc2-1.24.0-linux-x86_64/bin/ldc2 -Jviews -d-debug -g -unittest -w src/arg_parse.d src/run_analysis.d src/correct.d src/best.d src/weights.d src/calculation.d src/main.d src/read_data.d src/interpolate.o  -ofunittest
src/interpolate.o:interpolate.c:function interpolate: error: undefined reference to 'gsl_interp_steffen'
src/interpolate.o:interpolate.c:function interpolateSingleValue: error: undefined reference to 'gsl_interp_steffen'
collect2: error: ld returned 1 exit status
Error: /usr/bin/cc failed with status: 1
make: *** [test] Error 1
abrown25 commented 3 years ago

this means your version of the gsl is too old. Steffen interpolation was introduced in version 2.1. You can check your version with gsl --version

abrown25 commented 3 years ago

sorry, that should be gsl-config --version

XscapeCn commented 3 years ago

Thank you, I have already updated my gsl to 2.6, gsl-config --version is 2.6. And I compiled it in another PC, but when read .vcf.gz, it will send an error:

Failed to read phenotype IDs. invalid UTF-8sequence.

Thank you again!