rekado pushed a commit to branch master
in repository guix.
commit c527d36f0250b9815507e4ac28c3d7cfb6b87b20
Author: Ricardo Wurmus <[email protected]>
Date: Thu Nov 8 09:02:34 2018 +0100
gnu: java-picard-1.113: Use INVOKE.
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
---
gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++-----------------
1 file changed, 19 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e1ed711..70597e2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3476,26 +3476,28 @@ VCF.")
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "lib/jni")
(mkdir-p "jdk-src")
- (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
- "-xf" (assoc-ref inputs "jdk-src")))
- (zero? (system* "javah" "-jni"
- "-classpath" "classes"
- "-d" "lib/"
- "net.sf.samtools.util.zip.IntelDeflater"))
- (with-directory-excursion "src/c/inteldeflater"
- (zero? (system* "gcc" "-I../../../lib" "-I."
- (string-append "-I" (assoc-ref inputs
"jdk")
- "/include/linux")
-
"-I../../../jdk-src/src/share/native/common/"
-
"-I../../../jdk-src/src/solaris/native/common/"
- "-c" "-O3" "-fPIC" "IntelDeflater.c"))
- (zero? (system* "gcc" "-shared"
- "-o" "../../../lib/jni/libIntelDeflater.so"
- "IntelDeflater.o" "-lz" "-lstdc++"))))))
+ (invoke "tar" "--strip-components=1" "-C" "jdk-src"
+ "-xf" (assoc-ref inputs "jdk-src"))
+ (invoke "javah" "-jni"
+ "-classpath" "classes"
+ "-d" "lib/"
+ "net.sf.samtools.util.zip.IntelDeflater")
+ (with-directory-excursion "src/c/inteldeflater"
+ (invoke "gcc" "-I../../../lib" "-I."
+ (string-append "-I" (assoc-ref inputs "jdk")
+ "/include/linux")
+ "-I../../../jdk-src/src/share/native/common/"
+ "-I../../../jdk-src/src/solaris/native/common/"
+ "-c" "-O3" "-fPIC" "IntelDeflater.c")
+ (invoke "gcc" "-shared"
+ "-o" "../../../lib/jni/libIntelDeflater.so"
+ "IntelDeflater.o" "-lz" "-lstdc++"))
+ #t))
;; We can only build everything else after building the JNI library.
(add-after 'build-jni 'build-rest
(lambda* (#:key make-flags #:allow-other-keys)
- (zero? (apply system* `("ant" "all" ,@make-flags)))))
+ (apply invoke `("ant" "all" ,@make-flags))
+ #t))
(add-before 'build 'set-JAVA6_HOME
(lambda _
(setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
