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NGS Language Bindings
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Cannot build and install #25

Closed theo-allnutt-bioinformatics closed 4 years ago

theo-allnutt-bioinformatics commented 5 years ago

When making ncbi-vdb as per instructions, get his error:

/stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib/json-grammar.y:86.1-6: error: invalid directive: ‘%param’ /stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib/json-grammar.y:86.8-35: error: syntax error, unexpected {...} make[3]: [/stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib/json-grammar.c] Error 1 make[3]: Leaving directory `/stornext/HPCScratch/home/allnutt.t/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/obj/libs/klib' make[2]: [compile] Error 2 make[2]: Leaving directory /stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib' make[1]: *** [klib] Error 2 make[1]: Leaving directory/stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs' make: *** [libs] Error 2

kwrodarmer commented 5 years ago

What version of bison do you have?

theo-allnutt-bioinformatics commented 5 years ago

Bison 2.7

aboshkin commented 5 years ago

Upgrading to Bison 3.* should help. However, bison should not be invoked when doing a full build, the build should use the source-controlled bison-generated file instead. I am going to create an internal ticket to fix this.

If upgrading Bison is not an option, try this quick fix:

git checkout /stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib/json-grammar.c touch /stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib/json-grammar.c re-run the build

theo-allnutt-bioinformatics commented 5 years ago

Gives me this error:

$git checkout /stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb/libs/klib/json-grammar.c fatal: Not a git repository (or any parent up to mount point /stornext/HPCScratch) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

durbrow commented 5 years ago

cd /stornext/HPCScratch/home/allnutt.t/bin/ncbi/ncbi-vdb git checkout libs/klib/json-grammar.c

If your current working directory is not inside a git repository, git does not know what the repository is.

klymenko commented 4 years ago

@theo-allnutt-bioinformatics , do you still have problems?

theo-allnutt-bioinformatics commented 4 years ago

It's a long time ago now, I think I just gave up.