2022-11-29T19:46:44 sortmerna 4.2.0 -> 4.3.6 https://github.com/biocore/sortmerna/releases
2022-11-29T19:46:46 attrpath: sortmerna
2022-11-29T19:46:46 Checking auto update branch...
2022-11-29T19:46:46 No auto update branch exists
2022-11-29T19:46:50 [version] 
2022-11-29T19:47:03 [version] updated version and sha256
2022-11-29T19:47:03 [rustCrateVersion] 
2022-11-29T19:47:03 [rustCrateVersion] No cargoSha256 found
2022-11-29T19:47:03 [golangModuleVersion] 
2022-11-29T19:47:03 [golangModuleVersion] Not a buildGoModule package with vendorSha256
2022-11-29T19:47:03 [updateScript] 
2022-11-29T19:47:03 [updateScript] skipping because derivation has no updateScript
2022-11-29T19:47:03 
2022-11-29T19:47:03 [quotedUrls]
2022-11-29T19:47:03 [quotedUrls] nothing found to replace
2022-11-29T19:47:03 Diff after rewrites:
diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix
index 6884e1955f7..974894554d7 100644
--- a/pkgs/applications/science/biology/sortmerna/default.nix
+++ b/pkgs/applications/science/biology/sortmerna/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "sortmerna";
-  version = "4.2.0";
+  version = "4.3.6";
 
   src = fetchFromGitHub {
     repo = pname;
     owner = "biocore";
     rev = "v${version}";
-    sha256 = "0r91viylzr069jm7kpcgb45kagvf8sqcj5zc1af4arl9sgfs1f3j";
+    sha256 = "sha256-5sYnYmhCLdsfT6ih5CEBkYxfGkP8ZOSgTWU0kY2ZKTA=";
   };
 
   nativeBuildInputs = [ cmake pkg-config ];

2022-11-29T19:48:42 Received ExitFailure 100 when running
Raw command: /nix/store/6fr58pqy02hmgw1h7b9nqmv7vlp3v346-nix-2.3.15/bin/nix-build --option sandbox true --arg config "{ allowBroken = true; allowUnfree = true; allowAliases = false; }" --arg overlays "[ ]" -A sortmerna
nix build failed.
/build/source/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-parameter-Wunused-parameter]8;;]
  317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd)
      |                          ~~~~~~~~~~^~~~
/build/source/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-parameter-Wunused-parameter]8;;]
  317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd)
      |                                          ~~~~~~~~~~~~~~^~~
/build/source/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)':
/build/source/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-parameter-Wunused-parameter]8;;]
  540 | void Read::unmarshallJson(KeyValueDatabase & kvdb)
      |                           ~~~~~~~~~~~~~~~~~~~^~~~
/build/source/src/sortmerna/index.cpp: In member function 'void Index::load(uint32_t, uint32_t, std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&, Refstats&)':
/build/source/src/sortmerna/index.cpp:211:58: warning: dereferencing type-punned pointer will break strict-aliasing rules []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstrict-aliasing-Wstrict-aliasing]8;;]
  211 |                                         ((NodeElement *&)dst) += 4;
      |                                                          ^~~
/build/source/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstrict-aliasing-Wstrict-aliasing]8;;]
  257 |                                                                 ((NodeElement *&)dst) += 4;
      |                                                                                  ^~~
In file included from /build/source/include/kseq_load.hpp:40,
                 from /build/source/src/sortmerna/readstats.cpp:52:
/build/source/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-function-Wunused-function]8;;]
  171 |         static int kseq_read(kseq_t *seq)                                                                       \
      |                    ^~~~~~~~~
/build/source/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ'
  221 |         __KSEQ_READ
      |         ^~~~~~~~~~~
/build/source/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT'
   43 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
make[1]: *** [CMakeFiles/Makefile2:216: src/sortmerna/CMakeFiles/smr_objs.dir/all] Error 2
make: *** [Makefile:156: all] Error 2