Hi!
On Wed, 8 Jan 2025 22:02:10 +0100 =?utf-8?Q?=C3=89tienne?= Mollier
<[email protected]> wrote:
> This:
>
> > > WARNING: I tried to get the version of spades with: "/usr/bin/spades.py
> > > --version" and the output didn't match this regular expression:
> > > "SPAdes.*v([0-9\.]+)"
> > > ARIBA version: local
> > >
> > > External dependencies:
> > > bowtie2 2.5.4 /usr/bin/bowtie2
> > > cdhit 4.8.1 /usr/bin/cd-hit-est
> > > nucmer 3.1 /usr/bin/nucmer
> > > spades ERROR /usr/bin/spades.py
>
> heavily suggests that spades may have taken a hit at some point
> lately. I haven't investigated further what's up yet, just
> pinpointing what's off in the middle of the build output.
>
> Have a nice day, :)
> --
> .''`. Étienne Mollier <[email protected]>
> : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
> `. `' sent from /dev/pts/1, please excuse my verbosity
> `- on air: Spock's Beard - Edge Of The In Between
beside that, "exec" and "eval" changed semantic of the default locals namespace
in Python 3.13,
attached patch addresses this change ("exec" and "eval" usage can be avoided,
but the maintainer
seems to be far away).
Kind Regardsdiff -Nru --exclude changelog ariba-2.14.7+ds/debian/patches/py3.13.patch ariba-2.14.7+ds/debian/patches/py3.13.patch
--- ariba-2.14.7+ds/debian/patches/py3.13.patch 1970-01-01 00:00:00.000000000 +0000
+++ ariba-2.14.7+ds/debian/patches/py3.13.patch 2025-01-10 16:40:23.000000000 +0000
@@ -0,0 +1,22 @@
+--- a/ariba/versions.py
++++ b/ariba/versions.py
+@@ -34,9 +34,16 @@
+
+ for package in ['ariba', 'bs4', 'dendropy', 'pyfastaq', 'pymummer', 'pysam']:
+ try:
+- exec('import ' + package)
+- version = eval(package + '.__version__')
+- path = eval(package + '.__file__')
++ if sys.version_info[:2] >= (3, 13):
++ locals = {}
++ exec('import ' + package, locals=locals)
++ version = eval(package + '.__version__', locals=locals)
++ path = eval(package + '.__file__', locals=locals)
++ else:
++ exec('import ' + package)
++ version = eval(package + '.__version__')
++ path = eval(package + '.__file__')
++
+ except:
+ version = 'NOT_FOUND'
+ path = 'NOT_FOUND'
diff -Nru --exclude changelog ariba-2.14.7+ds/debian/patches/series ariba-2.14.7+ds/debian/patches/series
--- ariba-2.14.7+ds/debian/patches/series 2024-12-04 16:25:45.000000000 +0000
+++ ariba-2.14.7+ds/debian/patches/series 2025-01-10 16:40:23.000000000 +0000
@@ -6,3 +6,4 @@
run-debian-spades-wrapper.patch
python3.12.patch
python3.12_syntax_warning.patch
+py3.13.patch
