f57fc11d951807e19b20b5960e735fa50eaea279 braney Fri Jun 12 13:10:00 2026 -0700 Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> diff --git src/hg/mouseStuff/libScan/libScan.c src/hg/mouseStuff/libScan/libScan.c index 4ee35ef4a1f..f73d798eef2 100644 --- src/hg/mouseStuff/libScan/libScan.c +++ src/hg/mouseStuff/libScan/libScan.c @@ -1,183 +1,183 @@ /* libScan - Scan libraries to help find g' capped ones. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "jksql.h" #include "htmshell.h" int dotEvery = 0; void usage() /* Explain usage and exit. */ { errAbort( "libScan - Scan libraries to help find g' capped ones\n" "usage:\n" " libScan database output.html\n" "options:\n" " -dots=N - write a dot every N mrnas/ests\n" ); } char *entrezScript = "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4"; void printEntrezNucleotideUrl(FILE *f, char *accession) /* Print URL for Entrez browser on a nucleotide. */ { fprintf(f, "\"%s&db=n&term=%s\"", entrezScript, accession); } void dotOut() /* Put out a dot every now and then if user want's to. */ { static int mod = 1; if (dotEvery > 0) { if (--mod <= 0) { fputc('.', stdout); fflush(stdout); mod = dotEvery; } } } struct libInfo /* Info on one library. */ { struct libInfo *next; char *idString; /* Id as a string for hashing. */ char *name; /* Library name. */ char authorId[10]; /* Author ID - checked to make sure unique. */ boolean multiAuthor;/* More than one author? */ int mrnaCount; /* Number of mRNAs used. */ int estCount; /* Number of ESTs used. */ char sampleAcc[12]; /* Accession of one instance of library. */ char sampleDate[12]; /* Date of sample. */ }; boolean isOrestesForm(char *name) /* Is lib name in format that shows it's from Orestes project? */ { int i, len = strlen(name); if (len < 5 || len > 6) return FALSE; if (!isupper(name[0])) return FALSE; if (!isupper(name[1])) return FALSE; for (i=2; i<len; ++i) if (!isdigit(name[i])) return FALSE; return TRUE; } int libInfoCmpEstCount(const void *va, const void *vb) /* Compare to sort based on query. */ { const struct libInfo *a = *((struct libInfo **)va); const struct libInfo *b = *((struct libInfo **)vb); return b->estCount - a->estCount; } void libScan(char *database, char *outName) /* libScan - Scan libraries to help find g' capped ones. */ { struct sqlConnection *conn = sqlConnect(database); char query[256]; char **row; struct sqlResult *sr; struct libInfo *libList = NULL, *lib; struct hash *libHash = newHash(0); FILE *f = mustOpen(outName, "w"); boolean isEst; sqlSafef(query, sizeof query, "select id,name from library"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(lib); slAddHead(&libList, lib); hashAddSaveName(libHash, row[0], lib, &lib->idString); lib->name = cloneString(row[1]); } sqlFreeResult(&sr); slReverse(&libList); printf("Got %d libraries in %s\n", slCount(libList), database); sqlSafef(query, sizeof query, "select type,library,author,acc from mrna"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { dotOut(); lib = hashMustFindVal(libHash, row[1]); isEst = sameString(row[0], "EST"); if (lib->estCount + lib->mrnaCount == 0) { - strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc)); - strncpy(lib->authorId, row[2], sizeof(lib->authorId)); + safecpy(lib->sampleAcc, sizeof(lib->sampleAcc), row[3]); + safecpy(lib->authorId, sizeof(lib->authorId), row[2]); } else { if (isEst && lib->estCount == 0) - strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc)); + safecpy(lib->sampleAcc, sizeof(lib->sampleAcc), row[3]); if (!sameString(lib->authorId, row[2])) { if (!lib->multiAuthor) { lib->multiAuthor = TRUE; } } } if (isEst) ++lib->estCount; else ++lib->mrnaCount; } if (dotEvery) printf("\n"); sqlFreeResult(&sr); slSort(&libList, libInfoCmpEstCount); htmStart(f, "cDNA Libraries"); fprintf(f, "<PRE>"); for (lib = libList; lib != NULL; lib = lib->next) { if (lib->estCount > 50 && !isOrestesForm(lib->name)) { char date[16]; sqlSafef(query, sizeof query, "select gb_date from seq where acc = '%s'", lib->sampleAcc); sqlQuickQuery(conn, query, date, sizeof(date)); if (!startsWith("0000", date) && strcmp(date, "1999") > 0) { fprintf(f, "<A HREF="); printEntrezNucleotideUrl(f, lib->sampleAcc); fprintf(f, ">%s</A> ", lib->sampleAcc); fprintf(f, "%s %d\t%d\t%d\t%s\n", date, lib->multiAuthor, lib->mrnaCount, lib->estCount, lib->name); } } } htmEnd(f); sqlDisconnect(&conn); carefulClose(&f); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); dotEvery = cgiOptionalInt("dots", dotEvery); if (argc != 3) usage(); libScan(argv[1], argv[2]); return 0; }