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/geneBounds/motifSig/motifSig.c src/hg/geneBounds/motifSig/motifSig.c index 81e31754398..3370c6075d2 100644 --- src/hg/geneBounds/motifSig/motifSig.c +++ src/hg/geneBounds/motifSig/motifSig.c @@ -1,209 +1,209 @@ /* motifSig - Combine info from multiple control runs and main improbizer run. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "portable.h" #include "jksql.h" #include "improbRunInfo.h" #include "fa.h" void usage() /* Explain usage and exit. */ { errAbort( "motifSig - Combine info from multiple control runs and main improbizer run\n" "usage:\n" " motifSig output.tab seqDir motifDir controlDir(s)\n" ); } void countSeq(char *fileName, int *retSeqCount, int *retBaseCount) /* Count bases and sequences in fa file. */ { int seqCount = 0, baseCount = 0, oneSize; struct lineFile *lf = lineFileOpen(fileName, TRUE); DNA *dna; char *name; while (faSpeedReadNext(lf, &dna, &oneSize, &name)) { seqCount += 1; baseCount += oneSize; } lineFileClose(&lf); *retSeqCount = seqCount; *retBaseCount = baseCount; } #define maxMotifSize 256 struct motif /* Info on one motif. */ { char consensus[maxMotifSize+1]; /* Consensus sequence. */ float score; /* Motif Score */ float pos; /* Average position. */ float posSd; /* Standard deviation of positions. */ int size; /* Number of columns in motif - up to maxMotifSize. */ float profile[4][maxMotifSize]; /* Profile a,c,g,t probabilities. */ }; boolean readMotif(struct lineFile *lf, struct motif *m) /* Read five lines of motif info. */ { char *line; char *words[maxMotifSize+1]; int wordCount; int i,j; int colCount = 0; /* Get first line and parse it. */ ZeroVar(m); if (!lineFileNext(lf, &line, NULL)) return FALSE; wordCount = chopLine(line, words); if (wordCount < 6 || !sameString(words[1], "@")) errAbort("Bad line %d of %s", lf->lineIx, lf->fileName); m->score = atof(words[0]); m->pos = atof(words[2]); m->posSd = atof(words[4]); -strncpy(m->consensus, words[5], sizeof(m->consensus)); +safecpy(m->consensus, sizeof(m->consensus), words[5]); /* Get next lines with columns. */ for (i=0; i<4; ++i) { if (!lineFileNext(lf, &line, NULL)) errAbort("Unexpected end of file in %s", lf->fileName); wordCount = chopLine(line, words); if (i == 0) m->size = colCount = wordCount - 1; else lineFileExpectWords(lf, colCount+1, wordCount); for (j=0; j<colCount; ++j) m->profile[i][j] = atof(words[j+1]); } return TRUE; } struct improbRunInfo * analyseOneMotifRun(char *runName, char *seqDir, char *motifDir, int controlCount, char *controls[]) /* Bundle up data on one improbizer run and associated control runs. */ { char fileName[512]; char motifName[256]; int seqCount, baseCount; struct improbRunInfo *iriList = NULL, *iri; struct lineFile *lf = NULL; struct motif motif; int motifIx = 0; int i; float acc, best, mean, x; printf("%s\n", runName); /* Count bases in sequences - this will be used in each iri. */ sprintf(fileName, "%s/%s.fa", seqDir, runName); countSeq(fileName, &seqCount, &baseCount); /* Allocate iri and read the main run. */ sprintf(fileName, "%s/%s", motifDir, runName); lf = lineFileOpen(fileName, TRUE); while (readMotif(lf, &motif)) { AllocVar(iri); slAddTail(&iriList, iri); ++motifIx; snprintf(motifName, sizeof(motifName), "%s.%d", runName, motifIx); iri->name = cloneString(motifName); iri->seqCount = seqCount; iri->runScore = motif.score; iri->runPos = motif.pos; iri->runPosSd = motif.posSd; iri->columnCount = motif.size; iri->consensus = cloneString(motif.consensus); iri->aProb = CloneArray(motif.profile[0], motif.size); iri->cProb = CloneArray(motif.profile[1], motif.size); iri->gProb = CloneArray(motif.profile[2], motif.size); iri->tProb = CloneArray(motif.profile[3], motif.size); iri->controlCount = controlCount; AllocArray(iri->controlScores, controlCount); } lineFileClose(&lf); /* Read the control runs. */ for (i=0; i<controlCount; ++i) { sprintf(fileName, "%s/%s", controls[i], runName); lf = lineFileOpen(fileName, TRUE); for (iri = iriList; iri != NULL; iri = iri->next) { if (!readMotif(lf, &motif)) errAbort("%s doesn't contain the expected number of motifs", lf->fileName); iri->controlScores[i] = motif.score; } lineFileClose(&lf); } /* Calculate best and mean on control runs. */ for (iri = iriList; iri != NULL; iri = iri->next) { acc = best = 0; for (i=0; i<controlCount; ++i) { x = iri->controlScores[i]; acc += x; if (x > best) best = x; } iri->bestControlScore = best; iri->meanControlScore = acc/controlCount; } /* Calculate standard deviation of control runs. */ for (iri = iriList; iri != NULL; iri = iri->next) { acc = 0; mean = iri->meanControlScore; for (i=0; i<controlCount; ++i) { x = iri->controlScores[i] - mean; acc += x*x; } if (controlCount > 1) acc /= controlCount; iri->sdControlScore = sqrt(acc); } return iriList; } void motifSig(char *outName, char *seqDir, char *motifDir, int controlCount, char *controls[]) /* motifSig - Combine info from multiple control runs and main improbizer run. */ { FILE *f = mustOpen(outName, "w"); struct slName *mfList = listDir(motifDir, "*"), *mf; struct improbRunInfo *iriList = NULL, *iriSmallList = NULL, *iri; for (mf = mfList; mf != NULL; mf = mf->next) { iriSmallList = analyseOneMotifRun(mf->name, seqDir, motifDir, controlCount, controls); iriList = slCat(iriList, iriSmallList); } for (iri = iriList; iri != NULL; iri = iri->next) improbRunInfoTabOut(iri, f); carefulClose(&f); } int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); if (argc < 5) usage(); motifSig(argv[1], argv[2], argv[3], argc-4, argv+4); return 0; }