1 files changed, 78 insertions, 0 deletions
diff --git a/biology/htslib/patches/patch-hfile__libcurl.c b/biology/htslib/patches/patch-hfile__libcurl.c
new file mode 100644
index 00000000000..b7177535ba2
--- /dev/null
+++ b/biology/htslib/patches/patch-hfile__libcurl.c
@@ -0,0 +1,78 @@
+$NetBSD: patch-hfile__libcurl.c,v 1.1 2020/07/22 14:50:14 bacon Exp $
+
+# recent libcurl compatibility
+
+--- hfile_libcurl.c.orig	2019-12-19 09:54:30.000000000 +0000
++++ hfile_libcurl.c
+@@ -74,6 +74,10 @@ typedef struct {
+     unsigned int size;
+ } hdrlist;
+ 
++#ifndef ENOTRECOVERABLE
++#define ENOTRECOVERABLE EIO
++#endif
++
+ typedef struct {
+     hdrlist fixed;                   // List of headers supplied at hopen()
+     hdrlist extra;                   // List of headers from callback
+@@ -218,6 +222,8 @@ static int easy_errno(CURL *easy, CURLco
+         return EEXIST;
+ 
+     default:
++        hts_log_error("Libcurl reported error %d (%s)", (int) err,
++                      curl_easy_strerror(err));
+         return EIO;
+     }
+ }
+@@ -238,6 +244,8 @@ static int multi_errno(CURLMcode errm)
+         return ENOMEM;
+ 
+     default:
++        hts_log_error("Libcurl reported error %d (%s)", (int) errm,
++                      curl_multi_strerror(errm));
+         return EIO;
+     }
+ }
+@@ -797,9 +805,13 @@ static ssize_t libcurl_read(hFILE *fpv, 
+         fp->buffer.ptr.rd = buffer;
+         fp->buffer.len = nbytes;
+         fp->paused = 0;
+-        err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+-        if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
+-
++	if (! fp->finished) {
++            err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
++            if (err != CURLE_OK) {
++		errno = easy_errno(fp->easy, err);
++		return -1;
++	    }
++	}
+         while (! fp->paused && ! fp->finished) {
+             if (wait_perform(fp) < 0) return -1;
+         }
+@@ -1003,12 +1015,6 @@ static int restart_from_position(hFILE_l
+     }
+     temp_fp.nrunning = ++fp->nrunning;
+ 
+-    err = curl_easy_pause(temp_fp.easy, CURLPAUSE_CONT);
+-    if (err != CURLE_OK) {
+-        save_errno = easy_errno(temp_fp.easy, err);
+-        goto error_remove;
+-    }
+-
+     while (! temp_fp.paused && ! temp_fp.finished)
+         if (wait_perform(&temp_fp) < 0) {
+             save_errno = errno;
+@@ -1084,8 +1090,10 @@ static int libcurl_close(hFILE *fpv)
+     fp->buffer.len = 0;
+     fp->closing = 1;
+     fp->paused = 0;
+-    err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+-    if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
++    if (! fp->finished) {
++        err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
++        if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
++    }
+ 
+     while (save_errno == 0 && ! fp->paused && ! fp->finished)
+         if (wait_perform(fp) < 0) save_errno = errno;