rm abort and exit

Author: Zilong-Li

.Rbuildignore

@@ -3,7 +3,9 @@
 ^\.clangd$
 ^\.clang-format$
 ^.*\.tbi$
-^src/htslib-1.18/htscodecs/tests
+^src/htslib-1.21/htscodecs/tests
+^src/htslib-1.21/.*\.o$
+^src/.*\.o$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 \.github

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: vcfppR
 Title: Rapid Manipulation of the Variant Call Format (VCF)
-Version: 0.7.5
+Version: 0.7.6
 Authors@R: c(
     person("Zilong", "Li", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5859-2078")),

Makefile

@@ -30,7 +30,7 @@ check:
 
 check2: build
 	cd ..;\
-	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz  --as-cran
 
 clean:
 	cd ..;\

src/htslib-1.21/annot-tsv.c

@@ -124,7 +124,7 @@ error(const char *format, ...)
     vfprintf(stderr, format, ap);
     va_end(ap);
     fflush(stderr);
-    exit(EXIT_FAILURE);
+    /* exit(EXIT_FAILURE); */
 }
 
 static nbp_t *nbp_init(void)
@@ -986,7 +986,7 @@ int main(int argc, char **argv)
             case 's': args->src.fname = optarg; break;
             case 'f': args->transfer_str = optarg; break;
             case 'x': args->mode = PRINT_NONMATCHING; break;
-            case  4 : printf("\nVersion: %s\n%s\n",hts_version(),usage_text()); exit(EXIT_SUCCESS); break;
+            case  4 : printf("\nVersion: %s\n%s\n",hts_version(),usage_text()); break;
             case '?': // fall through
             default: error("\nVersion: %s\n%s\n",hts_version(),usage_text()); break;
         }

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr.c

@@ -160,7 +160,7 @@ unsigned char *rans_compress_O0_32x16(unsigned char *in,
                     RansEncPutSymbol_branched(&ransN[z-3], &ptr, s3);
                 }
             }
-            if (z < -1) abort();
+            if (z < -1) return NULL;
         }
     } else {
         // Branchless version optimises poorly with gcc unless we have
@@ -237,7 +237,7 @@ unsigned char *rans_compress_O0_32x16(unsigned char *in,
                     rp[3-k] += sy[k]->bias + q*sy[k]->cmpl_freq;
                 }
             }
-            if (z < -1) abort();
+            if (z < -1) return NULL;
         }
         ptr = (uint8_t *)ptr16;
     }

src/htslib-1.21/htscodecs/htscodecs/rANS_static32x16pr_neon.c

@@ -295,7 +295,7 @@ unsigned char *rans_compress_O0_32x16_neon(unsigned char *in,
             vst1q_u32(&R[z-3], Rv1);
             vst1q_u32(&R[z-7], Rv2);
         }
-        if (z < -1) abort();
+        if (z < -1) return NULL;
     }
     for (z = NX-1; z >= 0; z--)
       RansEncFlush(&R[z], &ptr);

src/htslib-1.21/htscodecs/htscodecs/varint2.h

@@ -181,26 +181,26 @@ static inline int var_put_u32(uint8_t *cp, const uint8_t *endp, uint32_t x) {
     uint8_t *op = cp;
 
     if (x < 177) {
-        if (endp && endp - cp < 1) abort();//return 0;
+        if (endp && endp - cp < 1) return 0;
         // 0 to 176 in single byte as-is
         *cp++ = x;
     } else if (x < 16561) {
-        if (endp && endp - cp < 2) abort();//return 0;
+        if (endp && endp - cp < 2) return 0;
         *cp++ = ((x-177)>>8)+177;
         *cp++ = x-177;
     } else if (x < 540849) {
-        if (endp && endp - cp < 3) abort();//return 0;
+        if (endp && endp - cp < 3) return 0;
         *cp++ = ((x-16561)>>16)+241;
         *cp++ = (x-16561)>>8;
         *cp++ = x-16561;
     } else if (x < (1<<24)) {
-        if (endp && endp - cp < 4) abort();//return 0;
+        if (endp && endp - cp < 4) return 0;
         *cp++ = 249;
         *cp++ = x>>16;
         *cp++ = x>>8;
         *cp++ = x;
     } else {
-        if (endp && endp - cp < 5) abort();//return 0;
+        if (endp && endp - cp < 5) return 0;
         *cp++ = 250;
         *cp++ = x>>24;
         *cp++ = x>>16;

src/htslib-1.21/htsfile.c

@@ -210,115 +210,8 @@ static void copy_raw(const char *srcfilename, const char *destfilename)
     free(buffer);
 }
 
-static void usage(FILE *fp, int status)
-{
-    fprintf(fp,
-"Usage: htsfile [-chHv] FILE...\n"
-"       htsfile --copy [-v] FILE DESTFILE\n"
-"Options:\n"
-"  -c, --view         Write textual form of FILEs to standard output\n"
-"  -C, --copy         Copy the exact contents of FILE to DESTFILE\n"
-"  -h, --header-only  Display only headers in view mode, not records\n"
-"  -H, --no-header    Suppress header display in view mode\n"
-"  -v, --verbose      Increase verbosity of warnings and diagnostics\n");
-    exit(status);
-}
 
 int main(int argc, char **argv)
 {
-    static const struct option options[] = {
-        { "copy", no_argument, NULL, 'C' },
-        { "header-only", no_argument, NULL, 'h' },
-        { "no-header", no_argument, NULL, 'H' },
-        { "view", no_argument, NULL, 'c' },
-        { "verbose", no_argument, NULL, 'v' },
-        { "help", no_argument, NULL, 2 },
-        { "version", no_argument, NULL, 1 },
-        { NULL, 0, NULL, 0 }
-    };
-
-    int c, i;
-
-    status = EXIT_SUCCESS;
-    while ((c = getopt_long(argc, argv, "cChHv", options, NULL)) >= 0)
-        switch (c) {
-        case 'c': mode = view_all; break;
-        case 'C': mode = copy; break;
-        case 'h': mode = view_headers; show_headers = 1; break;
-        case 'H': show_headers = 0; break;
-        case 'v': hts_verbose++; verbose++; break;
-        case 1:
-            printf(
-"htsfile (htslib) %s\n"
-"Copyright (C) 2024 Genome Research Ltd.\n",
-                   hts_version());
-            exit(EXIT_SUCCESS);
-            break;
-        case 2:   usage(stdout, EXIT_SUCCESS); break;
-        default:  usage(stderr, EXIT_FAILURE); break;
-        }
-
-    if (optind == argc) usage(stderr, EXIT_FAILURE);
-
-    if (mode == copy) {
-        if (optind + 2 != argc) usage(stderr, EXIT_FAILURE);
-        copy_raw(argv[optind], argv[optind + 1]);
-        return status;
-    }
-
-    for (i = optind; i < argc; i++) {
-        hFILE *fp = hopen(argv[i], "r");
-        if (fp == NULL) {
-            error("can't open \"%s\"", argv[i]);
-            continue;
-        }
-
-        if (mode == identify) {
-            htsFormat fmt;
-            if (hts_detect_format2(fp, argv[i], &fmt) < 0) {
-                error("detecting \"%s\" format failed", argv[i]);
-                hclose_abruptly(fp);
-                continue;
-            }
-
-            char *description = hts_format_description(&fmt);
-            printf("%s:\t%s\n", argv[i], description);
-            free(description);
-        }
-        else {
-            htsFile *hts = hts_hopen(fp, argv[i], "r");
-            if (hts) {
-                switch (hts_get_format(hts)->category) {
-                case sequence_data:
-                    view_sam(hts, argv[i]);
-                    break;
-                case variant_data:
-                    view_vcf(hts, argv[i]);
-                    break;
-                default:
-                    if (verbose)
-                        view_raw(fp, argv[i]);
-                    else {
-                        errno = 0;
-                        error("can't view \"%s\": unknown format", argv[i]);
-                    }
-                    break;
-                }
-
-                if (hts_close(hts) < 0) error("closing \"%s\" failed", argv[i]);
-                fp = NULL;
-            }
-            else if ((errno == EFTYPE || errno == ENOEXEC) && verbose)
-                view_raw(fp, argv[i]);
-            else
-                error("can't view \"%s\"", argv[i]);
-        }
-
-        if (fp && hclose(fp) < 0) error("closing \"%s\" failed", argv[i]);
-    }
-
-    if (fclose(stdout) != 0 && errno != EBADF)
-        error("closing standard output failed");
-
-    return status;
+    return 0;
 }

src/htslib-1.21/tabix.c

@@ -66,7 +66,7 @@ error(const char *format, ...)
     vfprintf(stderr, format, ap);
     va_end(ap);
     fflush(stderr);
-    exit(EXIT_FAILURE);
+    /* exit(EXIT_FAILURE); */
 }
 
 static void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) HTS_NORETURN
@@ -86,7 +86,7 @@ error_errno(const char *format, ...)
         fprintf(stderr, "\n");
     }
     fflush(stderr);
-    exit(EXIT_FAILURE);
+    /* exit(EXIT_FAILURE); */
 }
 
 

src/htslib-1.21/thread_pool.c

@@ -1520,7 +1520,7 @@ int main(int argc, char **argv) {
         fprintf(stderr, "ordered1        # Main thread with non-block API\n");
         fprintf(stderr, "ordered2        # Dispatch thread, blocking API\n");
         fprintf(stderr, "pipe            # Multi-stage pipeline, several queues\n");
-        exit(1);
+        return 1;
     }
 
     n = atoi(argv[2]);
@@ -1530,6 +1530,6 @@ int main(int argc, char **argv) {
     if (strcmp(argv[1], "pipe") == 0)      return test_pipe(n);
 
     fprintf(stderr, "Unknown sub-command\n");
-    exit(1);
+    return 1;
 }
 #endif