Debian Patches

Status for canu/2.3+dfsg-2

Patch Description Author Forwarded Bugs Origin Last update
libsnappy use system package for snappy Michael R. Crusoe <crusoe@debian.org> not-needed
stacktrace ignore broken GCC version check Michael R. Crusoe <crusoe@debian.org> not-needed
spelling typo fixes Michael R. Crusoe <crusoe@debian.org> yes
use-debian-mhap-at-runtime.patch Use mhap jar from /usr/share/java Afif Elghraoui <afif@debian.org> not-needed 2016-03-20
do-not-trust-errno-on-success.patch Do not infer I/O failure from a non-zero errno POSIX only guarantees that errno is set when a call fails; it is never
cleared on success and may be set spuriously by any successful call.
Since glibc 2.43 malloc() can set errno (e.g. ENOENT) even when the
allocation succeeds. meryl-utility instead decides that fopen(), ftello()
and fclose() failed whenever errno is non-zero after the call:
.
errno = 0;
FILE *F = fopen(pathname, "w");
if (errno)
fprintf(stderr, "Failed to open '%s' for writing: %s\n", ...), exit(1);
.
so on such systems 'canu -pacbio ...' dies immediately while creating the
seqStore, with "Failed to open './ecoli.seqStore.BUILDING/errorLog' for
writing: No such file or directory" even though the file was created.
.
Check the return value of the call instead, as done upstream in
meryl-utility commit 7b9d71f. Affects openInputFile(), openOutputFile(),
ftell(), closeFile(), writeBuffer::open(), compressedFileReader::close()
and compressedFileWriter::open()/close(), and the same pattern in
tgStore::openDB() and in the fopen() callers in correction/ and
overlapInCore/.		 Andreas Tille <tille@debian.org> yes 2026-11-04
mhap-needs-commons-io.patch Put commons-io on mhap's classpath The mhap jar is started with -jar, so only the jars listed in its manifest
Class-Path are available. That list has no commons-io, but mhap reads the
k-mer filter (and any other compressed input) through commons-compress,
which since 1.27 extends commons-io's BoundedInputStream. The mhap
precompute step therefore dies with
.
NoClassDefFoundError: org/apache/commons/io/input/BoundedInputStream
.
and canu aborts with "Mhap precompute jobs failed". Invoke the main class
with an explicit classpath instead so commons-io is resolvable.		 Andreas Tille <tille@debian.org> not-needed 2026-11-04
nonx86.patch Enable compilation on non-x86, non-arm, non-powerpc Michael R. Crusoe <crusoe@debian.org> no https://salsa.debian.org/med-team/parasail/-/blob/master/debian/patches/nonx86?ref_type=heads 2022-01-27

All known versions for source package 'canu'

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