A few minor patches for portability

[outpaddling]

--- ext/bifrost/src/strict_fstream.hpp.orig     2023-07-06 14:11:32 UTC
+++ ext/bifrost/src/strict_fstream.hpp
@@ -64,7 +64,7 @@ static std::string strerror()
     } else {
         return "Unknown error (" + std::to_string(err_num) + ")";
     }
-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__)
+#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) || defined(__NetBSD__)
 // XSI-compliant strerror_r()
     const int err_num = errno; // See above
     if (strerror_r(err_num, buff.data(), buff.size()) == 0) {

--- src/Bootstrap.h.orig        2020-04-01 16:56:42 UTC
+++ src/Bootstrap.h
@@ -1,6 +1,7 @@
 #ifndef KALLISTO_BOOTSTRAP_H
 #define KALLISTO_BOOTSTRAP_H
 
+#include <sys/types.h>
 #include <mutex>
 #include <thread>

--- 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"

--- ext/bifrost/src/libpopcnt.h.orig    2023-07-24 12:34:08.037669065 +0000
+++ ext/bifrost/src/libpopcnt.h
@@ -32,6 +32,8 @@
 #ifndef LIBPOPCNT_H
 #define LIBPOPCNT_H
 
+#ifndef __NetBSD__
+
 #include <stdint.h>
 
 #ifndef __has_builtin
@@ -584,4 +586,6 @@ static inline uint64_t popcnt(const void
 
 #endif
 
+#endif /* NetBSD */
+
 #endif /* LIBPOPCNT_H */