[med-svn] [Git][med-team/clustalo][master] Fix some issues with logging calls
Andreas Tille
gitlab at salsa.debian.org
Fri Apr 17 16:07:10 BST 2020
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 <tille at debian.org> 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 <matthew.fernandez at gmail.com>
+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
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