Hi @all, we have the problem, that the module reproducible will crash on the in house systems.

OS: CentOS Stream8

R: 4.2.2

Sample code:

library(msa)

se <- c("SEFGFEGFEGEF","SEFGFEGFEF","EGFEGEF")
msa(se,type = "protein")

Result, when calling "LANG=C Rscript /tmp/test.R" which contains the code above:

Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

use default substitution matrix
/usr/include/c++/8/backward/auto_ptr.h:198: std::auto_ptr< <template-parameter-1-1> >::element_type* std::auto_ptr< <template-parameter-1-1> >::operator->() const [with _Tp = clustalw::FileParser; std::auto_ptr< <template-parameter-1-1> >::element_type = clustalw::FileParser]: Assertion '_M_ptr != 0' failed.

Segfault

Have some body an hint, what can we do?

Hint: using "ClustalOmega" or "Muscle" will work, only "ClustalW" will trigger the crash.

Thanks