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-rw-r--r--gnu/packages/bioinformatics.scm35
1 files changed, 34 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b29ca67dbd..c076736da4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1628,7 +1628,40 @@ against local background noises.")
"/sources/shogun-" version ".tar.bz2"))
(sha256
(base32
- "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))))
+ "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
+ (modules '((guix build utils)
+ (ice-9 rdelim)))
+ (snippet
+ '(begin
+ ;; Remove non-free sources and files referencing them
+ (for-each delete-file
+ (find-files "src/shogun/classifier/svm/"
+ "SVMLight\\.(cpp|h)"))
+ (for-each delete-file
+ (find-files "examples/undocumented/libshogun/"
+ (string-append
+ "(classifier_.*svmlight.*|"
+ "evaluation_cross_validation_locked_comparison).cpp")))
+ ;; Remove non-free functions.
+ (define (delete-ifdefs file)
+ (with-atomic-file-replacement file
+ (lambda (in out)
+ (let loop ((line (read-line in 'concat))
+ (skipping? #f))
+ (if (eof-object? line)
+ #t
+ (let ((skip-next?
+ (or (and skipping?
+ (not (string-prefix?
+ "#endif //USE_SVMLIGHT" line)))
+ (string-prefix?
+ "#ifdef USE_SVMLIGHT" line))))
+ (when (or (not skipping?)
+ (and skipping? (not skip-next?)))
+ (display line out))
+ (loop (read-line in 'concat) skip-next?)))))))
+ (for-each delete-ifdefs (find-files "src/shogun/kernel/"
+ "^Kernel\\.(cpp|h)"))))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ;no check target