<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 1, 2020, at 00:27, Jeffrey Walton <<a href="mailto:noloader@gmail.com" class="">noloader@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">On Fri, May 1, 2020 at 3:05 AM Jeffrey Walton <</span><a href="mailto:noloader@gmail.com" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">noloader@gmail.com</a><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">> wrote:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class="">On Fri, May 1, 2020 at 2:14 AM Andreas Tille <<a href="mailto:andreas@fam-tille.de" class="">andreas@fam-tille.de</a>> wrote:<br class=""><blockquote type="cite" class=""><br class="">...<br class="">==13209== Process terminating with default action of signal 10 (SIGBUS)<br class="">==13209== at 0x12D5CC: PairDistances (pair_dist.c:346)<br class="">==13209== by 0x119410: AlignmentOrder (clustal-omega.c:835)<br class="">==13209== by 0x11A6C4: Align (clustal-omega.c:1221)<br class="">==13209== by 0x1171C8: MyMain (mymain.c:1192)<br class="">==13209== by 0x113CCC: main (main.cpp:469)<br class=""></blockquote><br class="">Here is line 346 in<br class=""><a href="https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346:" class="">https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346:</a><br class=""><br class=""> NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),<br class=""> "Ktuple-distance calculation progress", bPrintCR);<br class=""><br class="">For testing, change LogGetFP(&rLog, LOG_INFO) for stdout for testing. I.e.,<br class=""><br class=""> NewProgress(&prProgress, stdout,,<br class=""> "Ktuple-distance calculation progress", bPrintCR);<br class=""><br class="">It looks like LogGetFP retrieves an entry in an array of FILE*. From<br class="">https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/log.h:<br class=""><br class="">typedef struct {<br class=""> /* the higher the level, the more priority it has. numbers must be<br class=""> * sequential<br class=""> */<br class=""><br class=""> /* array of function pointers */<br class=""> void (*prFunc[LOG_NUM_LEVELS]) (FILE *prFP, char *pcFormat,<br class="">va_list rVArgList);<br class=""> FILE *prFP[LOG_NUM_LEVELS];<br class=""> char *prPrefix[LOG_NUM_LEVELS];<br class=""><br class=""> /* everything above this level will be printed */<br class=""> int iLogLevelEnabled;<br class="">} log_t;<br class=""><br class="">And https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/log.c:<br class=""><br class="">FILE *<br class="">LogGetFP(log_t *prLog, int iLevel)<br class="">{<br class=""> assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);<br class=""> return prLog->prFP[iLevel];<br class="">}<br class=""><br class="">That should help determine if something is sideways in the log_t structure.<br class=""></blockquote><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Also, I think this should be:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">FILE *<br class="">LogGetFP(log_t *prLog, int iLevel)<br class="">{<br class=""> assert(iLevel>=0 && iLevel<LOG_NUM_LEVELS);<br class=""> return prLog->prFP[iLevel];<br class="">}<br class=""></blockquote><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">That is, 'iLevel<LOG_NUM_LEVELS' (not 'iLevel<=LOG_NUM_LEVELS’).</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div></blockquote></div><br class=""><div class="">Some further patches attached:</div><div class=""> 1. the log level correction Jeff noted.</div><div class=""> 2. remove a prototype for a non-existent function</div><div class=""> 3. delete a lot of dead code, aiming to minimise the number of lines we have to suspect in ongoing debugging. This is for debugging only; not intended to be applied during packaging.</div><div class=""><br class=""></div><div class=""></div></body></html>