[Rscape] use .gitattributes to preserve CRLF line endings in patch (#…

…5385)

[skip ci]

R/Rscape/.gitattributes

@@ -0,0 +1 @@
+bundled/patches/allow-env-var-override-of-dirs.patch -text diff

R/Rscape/build_tarballs.jl

@@ -31,13 +31,6 @@ cd $WORKSPACE/srcdir/rscape*/
 # variables to override default directories for finding data params at
 # runtime instead of a hardcoded path (which doesn't work because that
 # is set to the srcdir during build)
-#
-# first convert src/msatree.c to LF line endings (from CRLF),
-# otherwise the patch doesn't apply
-cp src/msatree.c src/msatree.c.bak
-tr -d '\015' < src/msatree.c.bak > src/msatree.c
-#
-# now apply the patch
 atomic_patch -p1 ../patches/allow-env-var-override-of-dirs.patch
 
 update_configure_scripts

R/Rscape/bundled/patches/allow-env-var-override-of-dirs.patch

@@ -123,19 +123,19 @@ index a5e268e..b2691ba 100644
 --- a/src/msatree.c
 +++ b/src/msatree.c
 @@ -122,8 +122,11 @@ Tree_CreateExtFile(const ESL_MSA *msa, char **ret_treefile, char *errbuf, int ve
-   if ((status = esl_msafile_Write(msafp, (ESL_MSA *)msa, eslMSAFILE_AFA)) != eslOK) ESL_XFAIL(status, errbuf, "Failed to write AFA file\n");
-   fclose(msafp);
-
--  if (RSCAPE_BIN)                         // look for the installed executable
--    esl_sprintf(&cmd, "%s/FastTree", RSCAPE_BIN);  
-+  // override default RSCAPE_BIN with environment variable if it is set
-+  char *env_rscape_bin = getenv("RSCAPE_BIN");
-+  char *rscape_bin = env_rscape_bin ? env_rscape_bin : RSCAPE_BIN;
-+  if (rscape_bin)                         // look for the installed executable
-+    esl_sprintf(&cmd, "%s/FastTree", rscape_bin);
-   else
-     ESL_XFAIL(status, errbuf, "Failed to find FASTTREE executable\n");
-
+   if ((status = esl_msafile_Write(msafp, (ESL_MSA *)msa, eslMSAFILE_AFA)) != eslOK) ESL_XFAIL(status, errbuf, "Failed to write AFA file\n");
+   fclose(msafp);
+
+-  if (RSCAPE_BIN)                         // look for the installed executable
+-    esl_sprintf(&cmd, "%s/FastTree", RSCAPE_BIN);  
++  // override default RSCAPE_BIN with environment variable if it is set
++  char *env_rscape_bin = getenv("RSCAPE_BIN");
++  char *rscape_bin = env_rscape_bin ? env_rscape_bin : RSCAPE_BIN;
++  if (rscape_bin)                         // look for the installed executable
++    esl_sprintf(&cmd, "%s/FastTree", rscape_bin);
+   else
+     ESL_XFAIL(status, errbuf, "Failed to find FASTTREE executable\n");
+
 diff --git a/src/r2rdepict.c b/src/r2rdepict.c
 index b920439..ea3a9ba 100644
 --- a/src/r2rdepict.c