git: 8a2deaeb09da - main - biology/kallisto: Update to 0.50.1,1
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Date: Sat, 04 Nov 2023 13:15:27 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=8a2deaeb09da2b11c7061bd7120c9078717157ee
commit 8a2deaeb09da2b11c7061bd7120c9078717157ee
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-11-04 13:12:42 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-11-04 13:15:25 +0000
biology/kallisto: Update to 0.50.1,1
Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
---
biology/kallisto/Makefile | 3 +--
biology/kallisto/distinfo | 6 +++---
biology/kallisto/files/patch-src_main.cpp | 10 ++++++++++
3 files changed, 14 insertions(+), 5 deletions(-)
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 4ae2b8bd94ec..8774208d9097 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,7 +1,6 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
-DISTVERSION= 0.50.0
-PORTREVISION= 2
+DISTVERSION= 0.50.1
PORTEPOCH= 1
CATEGORIES= biology
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index e216bb4ae394..f01c0d8e6e1c 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1688395958
-SHA256 (pachterlab-kallisto-v0.50.0_GH0.tar.gz) = f9cc0058d08206cb6dde4a4dcaf8a778df5a939a6e021508eea9b00b0d6d5368
-SIZE (pachterlab-kallisto-v0.50.0_GH0.tar.gz) = 5939018
+TIMESTAMP = 1698923323
+SHA256 (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 030752bab3b0e33cd3f23f6d8feddd74194e5513532ffbf23519e84db2a86d34
+SIZE (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 5947303
diff --git a/biology/kallisto/files/patch-src_main.cpp b/biology/kallisto/files/patch-src_main.cpp
new file mode 100644
index 000000000000..2eadc428781c
--- /dev/null
+++ b/biology/kallisto/files/patch-src_main.cpp
@@ -0,0 +1,10 @@
+--- src/main.cpp.orig 2023-11-02 11:38:09 UTC
++++ src/main.cpp
+@@ -11,6 +11,7 @@
+ #include <limits>
+
+ #include <cstdio>
++#include <unistd.h> // rmdir()
+
+ #include "common.h"
+ #include "ProcessReads.h"