Andreas Tille pushed to branch master at Debian Med / clustalo
Commits: 474c3597 by Andreas Tille at 2020-04-17T17:06:56+02:00 Fix some issues with logging calls - - - - - 3 changed files: - debian/changelog - + debian/patches/clustalo-log-format-calls.patch - + debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +clustalo (1.2.4-6) UNRELEASED; urgency=medium + + [ Matthew Fernand ] + * Fix some issues with logging calls + + -- Andreas Tille <[email protected]> Fri, 17 Apr 2020 17:06:22 +0200 + clustalo (1.2.4-5) unstable; urgency=medium * Run example test from BioPython that seems to fail on mipsel ===================================== debian/patches/clustalo-log-format-calls.patch ===================================== @@ -0,0 +1,112 @@ +Author: Matthew Fernandez <[email protected]> +Date: Fri Apr 17 07:32:23 2020 -0700 +Description: fix mismatched logging arguments + + This change corrects some logging calls that were passing format strings that + did not align with their arguments. These issues were detected by tagging the + Log() function with __attribute__((format(printf, 3, 4))). + +--- a/src/clustal-omega.c ++++ b/src/clustal-omega.c +@@ -1327,7 +1327,7 @@ Align(mseq_t *prMSeq, + CKFREE(piOrderLR); + if (NULL != pdSeqWeights) + CKFREE(pdSeqWeights); +- Log(&rLog, LOG_INFO, "Computing new guide tree (iteration step %d)"); ++ Log(&rLog, LOG_INFO, "Computing new guide tree (iteration step %d)", iIterationCounter); + if (AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq, + ((SEQTYPE_PROTEIN == prMSeq->seqtype) && (TRUE == prOpts->bUseKimura)) ? PAIRDIST_SQUIDID_KIMURA : PAIRDIST_SQUIDID, + NULL, prOpts->pcDistmatOutfile, +--- a/src/clustal/hhalign_wrapper.c ++++ b/src/clustal/hhalign_wrapper.c +@@ -1041,7 +1041,7 @@ HHalignWrapper(mseq_t *prMSeq, int *piOr + int i, j; /* aux */ + + Log(&rLog, LOG_DEBUG, +- "merge profiles at node %d", iN, piOrderLR[riAux]); ++ "merge profiles at node %d", iN); + + /* iNodeCount - prMSeq->nseqs = total # of merge-nodes + * unless in profile/profile alignment mode +--- a/src/clustal/muscle_tree.c ++++ b/src/clustal/muscle_tree.c +@@ -763,10 +763,10 @@ ValidateNode(uint uNodeIndex, tree_t *tr + n3 = tree->m_uNeighbor3[uNodeIndex]; + + if (NULL_NEIGHBOR == n2 && NULL_NEIGHBOR != n3) { +- Log(&rLog, LOG_FATAL, "Tree::ValidateNode, n2=null, n3!=null", uNodeIndex); ++ Log(&rLog, LOG_FATAL, "Tree::ValidateNode(%u), n2=null, n3!=null", uNodeIndex); + } + if (NULL_NEIGHBOR == n3 && NULL_NEIGHBOR != n2) { +- Log(&rLog, LOG_FATAL, "Tree::ValidateNode, n3=null, n2!=null", uNodeIndex); ++ Log(&rLog, LOG_FATAL, "Tree::ValidateNode(%u), n3=null, n2!=null", uNodeIndex); + } + + if (n1 != NULL_NEIGHBOR) +@@ -1221,7 +1221,7 @@ GetGroupFromFile(FILE *fp, uint uNodeInd + ; + else if (NTT_Comma == NTT) { + if (ungetc(',', fp)==EOF) +- Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); ++ Log(&rLog, LOG_FATAL, "%s", "ungetc failed"); + return FALSE; + } else + Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected ')' or ',', got '%s'", szToken); +@@ -1248,7 +1248,7 @@ GetGroupFromFile(FILE *fp, uint uNodeInd + return TRUE; + } + if (ungetc(c, fp)==EOF) +- Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); ++ Log(&rLog, LOG_FATAL, "%s", "ungetc failed"); + + return FALSE; + } +@@ -1293,7 +1293,7 @@ FileSkipWhiteX(FILE *fp) + return TRUE; + if (!isspace(c)) { + if (ungetc(c, fp)==EOF) +- Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); ++ Log(&rLog, LOG_FATAL, "%s", "ungetc failed"); + break; + } + } +@@ -1383,7 +1383,7 @@ GetToken(FILE *fp, char szToken[], uint + case NTT_String: + if (0 != strchr("():;,", c)) { + if (ungetc(c, fp)==EOF) +- Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); ++ Log(&rLog, LOG_FATAL, "%s", "ungetc failed"); + return NTT_String; + } + if (isspace(c)) +--- a/src/clustal/seq.c ++++ b/src/clustal/seq.c +@@ -471,7 +471,7 @@ ReadSequences(mseq_t *prMSeq, char *seqf + } + if ((int)strlen(cur_seq)>iMaxSeqLen) { + Log(&rLog, LOG_ERROR, "Sequence '%s' has %d residues and is therefore longer than allowed (max. sequence length is %d)", +- cur_sqinfo.name, strlen(cur_seq), iMaxSeqLen); ++ cur_sqinfo.name, (int)strlen(cur_seq), iMaxSeqLen); + return -1; + } + if ((int)strlen(cur_seq)==0) { +--- a/src/clustal/util.c ++++ b/src/clustal/util.c +@@ -480,7 +480,7 @@ FileIsWritable(char *pcFileName) + } else { + bIsWritable = TRUE; + if (0 != fclose(prFilePointer)) { +- Log(&rLog, LOG_ERROR, "Couldn't close temporily created file %s. Expect trouble..."); ++ Log(&rLog, LOG_ERROR, "Couldn't close temporily created file %s. Expect trouble...", pcFileName); + } + } + +@@ -495,7 +495,7 @@ FileIsWritable(char *pcFileName) + */ + if (FALSE==bFileAlreadyExisted && TRUE==bIsWritable) { + if (0 != remove(pcFileName)) { +- Log(&rLog, LOG_ERROR, "Removing of temporarily created file %s failed. Expect trouble..."); ++ Log(&rLog, LOG_ERROR, "Removing of temporarily created file %s failed. Expect trouble...", pcFileName); + } + } + return bIsWritable; ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +clustalo-log-format-calls.patch View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/commit/474c3597061196fc39a1ffcbf036bb1f7d4a1a8a -- View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/commit/474c3597061196fc39a1ffcbf036bb1f7d4a1a8a You're receiving this email because of your account on salsa.debian.org.
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