From 7aa54350b9a7f4b1ba59fabaf8456f315981a908 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Tue, 3 Dec 2024 14:01:04 +0000
Subject: gn: vg: Remove commented-out code.

* gn/packages/bioinformatics.scm (vg)[arguments]: Remove commented-out
code.
---
 gn/packages/bioinformatics.scm | 36 ------------------------------------
 1 file changed, 36 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 397b38f..e0586fb 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2403,10 +2403,6 @@ in-memory footprint at the cost of packing and unpacking.")
                ((" \\$\\(LIB_DIR\\)/libdw.a")
                 (string-append " " (search-input-file inputs "/lib/libdw.so")))
 
-               ;; We need the Make.helper file in SDSL_DIR for gcsa2
-               ;((" \\$\\(LIB_DIR\\)/libsdsl.a")
-               ; (string-append " " (search-input-file inputs "/lib/libsdsl.so")))
-
                ((" \\$\\(LIB_DIR\\)/%divsufsort.a")
                 (string-append " " (dirname
                                      (search-input-file inputs "/lib/libdivsufsort.so"))
@@ -2445,37 +2441,6 @@ in-memory footprint at the cost of packing and unpacking.")
                (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}")
                 (dirname
                   (search-input-file inputs "/include/divsufsort.h"))))))
-         #;
-         (add-before 'patch-source 'use-shared-libvg
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (substitute* "Makefile"
-               (("libvg\\.a") "libvg.so")
-               ;; Have the linker find the shared library.
-               (("\\$\\(LIB_DIR\\)/libvg.\\$\\(SHARED_SUFFIX\\) \\$\\(LDFLAGS\\)")
-                "-lvg $(LDFLAGS)")
-               (("\\$\\(LDFLAGS\\) \\$\\(LIB_DIR\\)/libvg.so")
-                "$(LDFLAGS) -lvg"))
-             (setenv "LDFLAGS" (string-append "-Wl,-rpath="
-                                              (assoc-ref outputs "out") "/lib"))
-
-             ;; We need to tell a number of dependencies to build with -fPIC.
-             (substitute* "Makefile"
-               (("^CXXFLAGS := -O3")
-                (string-append "CFLAGS := -fPIC\n"
-                               "CXXFLAGS := -O3 -fPIC"))
-               (("^export CXXFLAGS")
-                (string-append "export CFLAGS\n"
-                               "$(info CFLAGS are $(CFLAGS))\n"
-                               "export CXXFLAGS"))
-               ((" \\$\\(LIB_DIR\\)/libjemalloc.a")
-                (string-append " " (assoc-ref inputs "jemalloc")
-                               "/lib/libjemalloc_pic.a")))
-             ;; We don't want to pull in all the global CXXFLAGS here.
-             (substitute* "deps/sublinear-Li-Stephens/makefile"
-               (("^CXXFLAGS:=") "CXXFLAGS:= -fPIC "))
-             ;; CMAKE_CXX_FLAGS aren't set globally.
-             (substitute* "deps/kff-cpp-api/CMakeLists.txt"
-               (("CMAKE_CXX_FLAGS \"") "CMAKE_CXX_FLAGS \" -fPIC "))))
          (add-after 'unpack 'dont-build-shared-vgio
            (lambda _
              ;; vg will link with libvgio and fail the 'validate-runpath phase.
@@ -2529,7 +2494,6 @@ in-memory footprint at the cost of packing and unpacking.")
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
                (install-file "bin/vg" (string-append out "/bin"))
-               ;(install-file "lib/libvg.so" (string-append out "/lib"))
                (for-each
                  (lambda (file)
                    (install-file file (string-append out "/share/man/man1")))
-- 
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