guix_mirror_bot pushed a commit to branch master
in repository guix.
commit ff6b3eb2794264dbc6e81289da53d36881d60e8c
Author: Andreas Enge <[email protected]>
AuthorDate: Thu Oct 23 21:41:34 2025 +0200
gnu: Remove htslib-for-stringtie.
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Delete variable.
* gnu/packages/patches/htslib-for-stringtie.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.
Change-Id: Idbf3fa982895baed97913e08650cbff6947e8182
---
gnu/local.mk | 1 -
gnu/packages/bioinformatics.scm | 12 ------------
gnu/packages/patches/htslib-for-stringtie.patch | 26 -------------------------
3 files changed, 39 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 7601067a84..2d059f3535 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1574,7 +1574,6 @@ dist_patch_DATA =
\
%D%/packages/patches/highlight-gui-data-dir.patch \
%D%/packages/patches/hplip-usb-timeout.patch \
%D%/packages/patches/http-parser-CVE-2020-8287.patch \
- %D%/packages/patches/htslib-for-stringtie.patch \
%D%/packages/patches/hubbub-sort-entities.patch \
%D%/packages/patches/hueplusplus-mbedtls.patch \
%D%/packages/patches/hugs-fix-build.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c726dcf376..8951d3377b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9662,18 +9662,6 @@ data. It also provides the @command{bgzip},
@command{htsfile}, and
(base32
"1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
-(define htslib-for-stringtie
- (package
- (inherit htslib-1.12)
- (source (origin
- (inherit (package-source htslib-1.12))
- (patches
- (search-patches "htslib-for-stringtie.patch"))))
- (arguments
- `(#:configure-flags '("--with-libdeflate")))
- (inputs
- (list bzip2 libdeflate openssl))))
-
(define-public idr
(package
(name "idr")
diff --git a/gnu/packages/patches/htslib-for-stringtie.patch
b/gnu/packages/patches/htslib-for-stringtie.patch
deleted file mode 100644
index 3e6cd5bb63..0000000000
--- a/gnu/packages/patches/htslib-for-stringtie.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-These changes are commits d7e357946ead219b81cc1becbe0de8a99d96ca84 and
-8ed0daa39bc662defa99507f926815431056543a in
-https://github.com/samtools/htscodecs. The stringtie package expects these
-changes to have been applied.
-
-diff -ru htslib-1.12/htscodecs/htscodecs/tokenise_name3.c
stringtie-2.2.0/htslib/htscodecs/htscodecs/tokenise_name3.c
---- a/htscodecs/htscodecs/tokenise_name3.c 2021-02-22 13:07:06.000000000
+0100
-+++ b/htscodecs/htscodecs/tokenise_name3.c 2021-12-04 19:27:39.000000000
+0100
-@@ -211,7 +211,7 @@
- if (!ctx) return NULL;
- ctx->max_names = max_names;
- pthread_setspecific(tok_key, ctx);
-- } else if (ctx->max_names < max_names) {
-+ } else if (ctx->max_names < max_names+1) {
- ctx = realloc(ctx, sizeof(*ctx) + ++max_names*sizeof(*ctx->lc));
- if (!ctx) return NULL;
- ctx->max_names = max_names;
-@@ -1058,6 +1058,8 @@
- tok = decode_token_type(ctx, ntok);
- //fprintf(stderr, "Tok %d = %d\n", ntok, tok);
-
-+ ctx->lc[cnum].last_ntok = 0;
-+
- switch (tok) {
- case N_CHAR:
- if (len+1 >= name_len) return -1;
\ No newline at end of file
