Your message dated Sun, 30 Jun 2024 18:18:13 +0530
with message-id <cf49311a-f89e-4670-90ac-3987d9c67...@riseup.net>
and subject line Re: Bug#993809: bullseye-pu: package segemehl/0.3.4-3+deb11u1
(Pre-approval)
has caused the Debian Bug report #993809,
regarding bullseye-pu: package segemehl/0.3.4-3+deb11u1 (Pre-approval)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
993809: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=993809
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
Tags: bullseye
User: release.debian....@packages.debian.org
Usertags: pu
X-Debbugs-Cc: nil...@debian.org
[ Reason ]
The package segfauls to !amd64 and !i386 architectures. The version in
bullseye does not have autopkgtests, when we added those and uploaded
_after_ the bullseye release, tests were segfaulting on arm64, ppc64el
and armhf. Note that there has been no new upstream release, just test
addition with a few cosmetics.
Unfortunantely, the failing logs of the 0.3.4-4 version have disappeared
from here[1]
But, trying on a arm64 porter box confirms the experience.
% ./segemehl -x index.idx -d seq1.fa
[SEGEMEHL] Mon Sep 6 18:29:55 2021: reading database sequences.
zsh: segmentation fault ./segemehl -x index.idx -d seq1.fa
% ./segemehl -i index.idx -d seq1.fa -q myseq.fa > mymap.sam
[SEGEMEHL] Mon Sep 6 18:44:08 2021: reading queries in 'myseq.fa'.
...............this keeps running forever
This has been fixed in unstable with the relevant patch, and upload[2]
0.3.4-5 and it migrated to testing after everything passes
[1]: https://ci.debian.net/data/autopkgtest/unstable/arm64/s/segemehl/
[2]:
https://tracker.debian.org/news/1251311/accepted-segemehl-034-5-source-into-unstable/
Since I noticed and fixed it before any bug was filed, there does not
exist a corresponding RC bug in the database. Let me know if I should
file one and process BTS commands on that.
[ Impact ]
Users will find a broken segfaulting package on !amd64 and !i386
machines
[ Tests ]
Autopkgtests have been added. I've manually run them on porter boxes,
and it looks good (as it should)
The revision in unstable also has tests passing
https://ci.debian.net/data/autopkgtest/unstable/arm64/s/segemehl/14839955/log.gz
[ Risks ]
Being a leaf package with a not-very-high popcon, risk is pretty low
[ Checklist ]
[x] *all* changes are documented in the d/changelog
[x] I reviewed all changes and I approve them
[x] attach debdiff against the package in stable
[x] the issue is verified as fixed in unstable
diff -Nru segemehl-0.3.4/debian/changelog segemehl-0.3.4/debian/changelog
--- segemehl-0.3.4/debian/changelog 2021-02-18 15:14:26.000000000 +0530
+++ segemehl-0.3.4/debian/changelog 2021-09-06 23:46:30.000000000 +0530
@@ -1,3 +1,11 @@
+segemehl (0.3.4-3+deb11u1) bullseye; urgency=medium
+
+ * d/p/arm64.patch: Fix autopkgtest segaults on !amd64 and !i386
+ + Change the signed-ness for needed chars to fix segfault
+ * Add autopkgtests
+
+ -- Nilesh Patra <nil...@debian.org> Mon, 06 Sep 2021 23:46:30 +0530
+
segemehl (0.3.4-3) unstable; urgency=medium
* Team Upload.
diff -Nru segemehl-0.3.4/debian/examples segemehl-0.3.4/debian/examples
--- segemehl-0.3.4/debian/examples 1970-01-01 05:30:00.000000000 +0530
+++ segemehl-0.3.4/debian/examples 2021-09-06 23:45:58.000000000 +0530
@@ -0,0 +1 @@
+debian/tests/data/*
\ No newline at end of file
diff -Nru segemehl-0.3.4/debian/patches/arm64.patch
segemehl-0.3.4/debian/patches/arm64.patch
--- segemehl-0.3.4/debian/patches/arm64.patch 1970-01-01 05:30:00.000000000
+0530
+++ segemehl-0.3.4/debian/patches/arm64.patch 2021-09-06 23:43:50.000000000
+0530
@@ -0,0 +1,75 @@
+Description: Change the signed-ness for several chars to fix segfault
+Author: Nilesh Patra <nil...@debian.org>
+Last-Update: 2021-08-24
+--- a/libs/biofiles.c
++++ b/libs/biofiles.c
+@@ -1916,7 +1916,7 @@
+ Uint max, Uint *minlen, Uint *maxlen, unsigned char *minq, unsigned char
*maxq)
+ {
+
+- char ch;
++ signed char ch;
+ char idchar=0;
+ int ret=0;
+ off_t curseqoffset, lastindexoffset=0;
+@@ -2515,7 +2515,7 @@
+ {
+
+ FILE *fp;
+- char ch;
++ signed char ch;
+ char *buffer;
+ char *descrbuffer = NULL;
+ char *seqbuffer = NULL;
+--- a/libs/fileio.c
++++ b/libs/fileio.c
+@@ -498,7 +498,7 @@
+ void
+ bl_freplacestr(char *filename, char *str, Uint len, char stop){
+ int i = 0;
+- char ch;
++ signed char ch;
+ FILE *fp;
+
+ fp = fopen(filename, "rb+");
+@@ -523,7 +523,8 @@
+
+ int
+ bl_fgets(void *space, FILE *fp, char **str) {
+- char ch, *buffer;
++ signed char ch;
++ char *buffer;
+ size_t buffersize = MAXBUFFERSIZE;
+ size_t len = 0;
+
+@@ -549,7 +550,7 @@
+ char*
+ readfile(void* space, char* filename, size_t* strlen) {
+
+- char ch;
++ signed char ch;
+ char *buffer;
+ FILE *fp;
+ size_t buffersize = MAXBUFFERSIZE;
+--- a/libs/merge.c
++++ b/libs/merge.c
+@@ -596,7 +596,7 @@
+ if (!file->complete && !file->eof){
+
+ #ifndef FILEBUFFEREDMERGE
+- char ch;
++ signed char ch;
+ Uint buffersize = 1024;
+ buffer = ALLOCMEMORY(NULL, NULL, char, buffersize);
+ len = 0;
+--- a/libs/samheader.c
++++ b/libs/samheader.c
+@@ -460,7 +460,7 @@
+ {
+ FILE *fp;
+ off_t offset = 0;
+- char ch;
++ signed char ch;
+ char *buffer;
+ // char *descrbuffer = NULL;
+ // char *seqbuffer = NULL;
diff -Nru segemehl-0.3.4/debian/patches/series
segemehl-0.3.4/debian/patches/series
--- segemehl-0.3.4/debian/patches/series 2021-02-18 15:04:21.000000000
+0530
+++ segemehl-0.3.4/debian/patches/series 2021-09-06 23:41:48.000000000
+0530
@@ -1,2 +1,3 @@
rpath.patch
cross.patch
+arm64.patch
diff -Nru segemehl-0.3.4/debian/tests/control
segemehl-0.3.4/debian/tests/control
--- segemehl-0.3.4/debian/tests/control 1970-01-01 05:30:00.000000000 +0530
+++ segemehl-0.3.4/debian/tests/control 2021-09-06 23:45:58.000000000 +0530
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff -Nru segemehl-0.3.4/debian/tests/data/myseq.fa
segemehl-0.3.4/debian/tests/data/myseq.fa
--- segemehl-0.3.4/debian/tests/data/myseq.fa 1970-01-01 05:30:00.000000000
+0530
+++ segemehl-0.3.4/debian/tests/data/myseq.fa 2021-09-06 23:45:20.000000000
+0530
@@ -0,0 +1,2 @@
+>myseq
+ATGCGACTCAGACGACGACGACGACGAGACTAAGCAGACATCAGCAGACGACGACGCATACGACGATA
\ No newline at end of file
diff -Nru segemehl-0.3.4/debian/tests/data/seq1.fa
segemehl-0.3.4/debian/tests/data/seq1.fa
--- segemehl-0.3.4/debian/tests/data/seq1.fa 1970-01-01 05:30:00.000000000
+0530
+++ segemehl-0.3.4/debian/tests/data/seq1.fa 2021-09-06 23:45:20.000000000
+0530
@@ -0,0 +1,2 @@
+>index1
+ATGCATGCATGCATTTAGAGACAGCAGACGATACGACTACACAGCATCAACGACATACGACATCAGACGAACAAAAAAAAAAAAAGATCATCAGAATGGCATGGCATGACTCGACATCGACATCAGACATCAGAAATCAGACTAAGCATAGCATAGAATCAATACGACGACATAGATAGATAGATAAGCAGACTAAGCATACAGCACATAGCATAGACGAATAGCATACGACATAGAATAGATATCAGCA
\ No newline at end of file
diff -Nru segemehl-0.3.4/debian/tests/data/seq2.fa
segemehl-0.3.4/debian/tests/data/seq2.fa
--- segemehl-0.3.4/debian/tests/data/seq2.fa 1970-01-01 05:30:00.000000000
+0530
+++ segemehl-0.3.4/debian/tests/data/seq2.fa 2021-09-06 23:45:20.000000000
+0530
@@ -0,0 +1,2 @@
+>index2
+ATGCTACGACGACGACGAGAAGAGAGAGAAAAAAAAAAATACGACATCAGACTACGACATACTACAGACTACAGCATCAGAATAG
\ No newline at end of file
diff -Nru segemehl-0.3.4/debian/tests/run-unit-test
segemehl-0.3.4/debian/tests/run-unit-test
--- segemehl-0.3.4/debian/tests/run-unit-test 1970-01-01 05:30:00.000000000
+0530
+++ segemehl-0.3.4/debian/tests/run-unit-test 2021-09-06 23:45:58.000000000
+0530
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+pkg=segemehl
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+#do_stuff_to_test_package#
+segemehl -x index.idx -d seq1.fa
+segemehl -i index.idx -d seq1.fa -q myseq.fa > mymap.sam
+segemehl -S -i index.idx -d seq1.fa -q seq2.fa > my.sngl.bed
+[ -s "mymap.sam" ] && [ -s "index.idx" ] && [ -s "my.sngl.bed" ] || exit 1 &&
echo "PASS Test"
\ No newline at end of file
--- End Message ---
--- Begin Message ---
On 6/30/24 2:02 AM, Jonathan Wiltshire wrote:
Hi,
This request was approved for 11.10 but not uploaded in time; is it still
relevant for 11.11, the planned final point release for bullseye?
Thanks,
This request was approved 2 years after me asking if I should go ahead with the
p-u. Due to the
delay, I have lost interest (and time too) to do anything about it.
Given that no user reported a bug for the stable version of this package, I
suppose this is redundant
at this point and can be closed. Hence, I'm going ahead w/ doing so.
Thanks
--- End Message ---
