[Debian-med-packaging] Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)

[Jeffrey Walton]

On Fri, May 1, 2020 at 2:14 AM Andreas Tille <andreas at fam-tille.de> wrote:
>
>  ...
> ==13209== Process terminating with default action of signal 10 (SIGBUS)
> ==13209==    at 0x12D5CC: PairDistances (pair_dist.c:346)
> ==13209==    by 0x119410: AlignmentOrder (clustal-omega.c:835)
> ==13209==    by 0x11A6C4: Align (clustal-omega.c:1221)
> ==13209==    by 0x1171C8: MyMain (mymain.c:1192)
> ==13209==    by 0x113CCC: main (main.cpp:469)

Here is line 346 in
https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346:

            NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
                        "Ktuple-distance calculation progress", bPrintCR);

For testing, change LogGetFP(&rLog, LOG_INFO) for stdout for testing. I.e.,

            NewProgress(&prProgress, stdout,,
                        "Ktuple-distance calculation progress", bPrintCR);

It looks like LogGetFP retrieves an entry in an array of FILE*. From
https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/log.h:

typedef struct {
    /* the higher the level, the more priority it has. numbers must be
     *  sequential
     */

    /* array of function pointers */
    void (*prFunc[LOG_NUM_LEVELS]) (FILE *prFP, char *pcFormat,
va_list rVArgList);
    FILE *prFP[LOG_NUM_LEVELS];
    char *prPrefix[LOG_NUM_LEVELS];

    /* everything above this level will be printed */
    int iLogLevelEnabled;
} log_t;

And https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/log.c:

FILE *
LogGetFP(log_t *prLog, int iLevel)
{
    assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);
    return prLog->prFP[iLevel];
}

That should help determine if something is sideways in the log_t structure.

Jeff