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cfstream's Introduction

Biocaml - The OCaml Bioinformatics Library

DESCRIPTION

Biocaml aims to be a high-performance user-friendly library for Bioinformatics. See the website for detailed API documentation. We welcome contributors and feedback from users. Please contact us with any comments and suggestions for features you would like added.

INSTALLATION

See INSTALL file.

TESTING

dune runtest        # for inline tests
dune run_test_suite # for test suite tests

LICENSE

The Biocaml library is distributed according to the LGPL + linking exception terms as defined in the LICENSE file, which you should have received a copy of along with this library.

CONTACT

Ashish Agarwal: [email protected]
Website: http://biocaml.org
Mailing List: http://groups.google.com/group/biocaml

cfstream's People

Contributors

agarwal avatar drup avatar kit-ty-kate avatar mbacarella avatar pveber avatar rleonid avatar xclerc avatar

Stargazers

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cfstream's Issues

make ounit an optional dependency for opam

We only use ounit to write tests in app/cfstream_test. Should be possible to tell jbuilder this so that the .install file it generates won't include it. Also update the .opam file to declare ounit as test-time dependency.

fix build system

We should switch to solvuu-build.

In particular, there is currently a bug in our OMake based build. The clean command doesn't remove _build.

build error related to Caml.Not_found

$ jbuilder build --dev @install
      ocamlc lib/.CFStream.objs/CFStream__CFStream_stream.{cmo,cmt} (exit 2) ...
 -c -impl lib/CFStream_stream.ml)
File "lib/CFStream_stream.ml", line 70, characters 16-30:
Error: Unbound constructor Caml.Not_found

avoid warnings

Our new build config reveals several warnings:

$ make
...
ocamlbuild -use-ocamlfind -plugin-tag "package(solvuu-build)" ./cfstream.cma
Finished, 0 targets (0 cached) in 00:00:00.
+ ocamlfind ocamlc -annot -bin-annot -c -g -I lib -o lib/CFStream_stream.cmo -short-paths -strict-sequence -thread -w A-4-33-41-42-44-45-48 -package core_kernel lib/CFStream_stream.ml
File "lib/CFStream_stream.ml", line 496, characters 18-22:
Warning 6: label f was omitted in the application of this function.
File "lib/CFStream_stream.ml", line 521, characters 2-8:
Warning 6: label f was omitted in the application of this function.
File "lib/CFStream_stream.ml", line 550, characters 32-52:
Warning 3: deprecated: Core_kernel.Std.Hashtbl.Poly.replace
[since 2015-10] Use set instead
File "lib/CFStream_stream.ml", line 623, characters 6-21:
Warning 6: label f was omitted in the application of this function.
File "lib/CFStream_stream.ml", line 631, characters 6-21:
Warning 6: label f was omitted in the application of this function.
File "lib/CFStream_stream.ml", line 61, characters 11-12:
Warning 27: unused variable x.
File "lib/CFStream_stream.ml", line 524, characters 11-12:
Warning 27: unused variable i.
Finished, 7 targets (0 cached) in 00:00:03.
rm -f cfstream.cma
ocamlbuild -use-ocamlfind -plugin-tag "package(solvuu-build)" app/cfstream-test.byte
Finished, 0 targets (0 cached) in 00:00:00.
+ ocamlfind ocamlc -annot -bin-annot -g -I lib -o app/cfstream-test.byte -short-paths -strict-sequence -thread -w A-4-33-41-42-44-45-48 -package core_kernel,oUnit -linkpkg ./cfstream.cma app/cfstream_test.ml
File "app/cfstream_test.ml", line 6, characters 51-59:
Warning 6: label f was omitted in the application of this function.
File "app/cfstream_test.ml", line 99, characters 22-26:
Warning 6: label n was omitted in the application of this function.
File "app/cfstream_test.ml", line 105, characters 22-26:
Warning 6: label n was omitted in the application of this function.
File "app/cfstream_test.ml", line 139, characters 10-14:
Warning 6: label f was omitted in the application of this function.
File "app/cfstream_test.ml", line 153, characters 10-20:
Warning 6: label f was omitted in the application of this function.
Finished, 8 targets (7 cached) in 00:00:01.

avoid old operator from Core

File "test_stream.ml", line 172, characters 35-37:
Warning 3: deprecated: Core_kernel.Std.|!
[since 2016-07] Use [ |> ]

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