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authorpjotrp2017-02-02 08:15:18 +0000
committerpjotrp2017-02-02 08:15:18 +0000
commitea1ce997a5e43e1993864464e1a1d45e9b20c8db (patch)
tree09f8c17e96d86ef3ef9602da4ce05ce6f44a2abb
parent0c6ee6e845def194d50021eec528059671e04cd3 (diff)
downloadguix-bioinformatics-ea1ce997a5e43e1993864464e1a1d45e9b20c8db.tar.gz
Patching Druntime for sambamba
-rw-r--r--gn/packages/bioinformatics.scm2
-rw-r--r--gn/packages/ldc.scm9
-rw-r--r--ldc-druntime-finiTLSRanges.patch24
3 files changed, 30 insertions, 5 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 4ded90e..2dcaf62 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -924,7 +924,7 @@ association studies (GWAS).")
(let ((commit "91096e78c81162f855b1044a4b2d41895bd27262"))
(package
(name "sambamba")
- (version (string-append "0.6.6-pre1-" (string-take commit 7)))
+ (version (string-append "0.6.6-pre2-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
diff --git a/gn/packages/ldc.scm b/gn/packages/ldc.scm
index 3fb77b7..fec94e9 100644
--- a/gn/packages/ldc.scm
+++ b/gn/packages/ldc.scm
@@ -177,6 +177,7 @@
"https://github.com/ldc-developers/druntime/archive/ldc-v"
version2 ".tar.gz"))
(file-name (string-append "ldc-druntime-" version2 ".tar.gz"))
+ (patches (search-patches "ldc-druntime-finiTLSRanges.patch"))
(sha256
(base32
"07qvrqj6vgakd6qr4x5f70w6zwkzd1li5x8i1b5ywnds1z5lnfp6"))))
@@ -202,10 +203,10 @@
(uri (string-append
"https://github.com/dlang/tools/archive/"
version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0ryn4fv1mj8c8d7y4lrr43baahl3z7sk5bryj9kd829paz573va6"))))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0ryn4fv1mj8c8d7y4lrr43baahl3z7sk5bryj9kd829paz573va6"))))
(build-system gnu-build-system)
(arguments
'(#:phases
diff --git a/ldc-druntime-finiTLSRanges.patch b/ldc-druntime-finiTLSRanges.patch
new file mode 100644
index 0000000..152f341
--- /dev/null
+++ b/ldc-druntime-finiTLSRanges.patch
@@ -0,0 +1,24 @@
+diff --git a/src/rt/sections_elf_shared.d b/src/rt/sections_elf_shared.d
+index a1ea73a..243e3f6 100644
+--- a/src/rt/sections_elf_shared.d
++++ b/src/rt/sections_elf_shared.d
+@@ -149,7 +149,8 @@ version (Shared)
+
+ void finiTLSRanges(Array!(ThreadDSO)* tdsos)
+ {
+- tdsos.reset();
++ // Disabling like static version - not sure this one is misbehaving though
++ // tdsos.reset();
+ }
+
+ void scanTLSRanges(Array!(ThreadDSO)* tdsos, scope ScanDG dg) nothrow
+@@ -234,7 +235,8 @@ else
+
+ void finiTLSRanges(Array!(void[])* rngs)
+ {
+- rngs.reset();
++ // Throws exception, see https://github.com/lomereiter/sambamba/issues/219#issuecomment-275838455
++ // rngs.reset();
+ }
+
+ void scanTLSRanges(Array!(void[])* rngs, scope ScanDG dg) nothrow