[From nobody Wed Sep 9 13:21:06 2026 Received: (at submit) by bugs.debian.org; 6 Sep 2026 18:13:18 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-118.2 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,HAS_PACKAGE,SPF_HELO_NONE, SPF_PASS,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 40; hammy, 150; neutral, 81; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <maxy@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:35348) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <maxy@debian.org>) id 1x3HMk-003pa4-25 for submit@bugs.debian.org; Sun, 06 Sep 2026 18:13:18 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Type:MIME-Version:Message-ID: Subject:To:From:Date:Reply-To:Cc:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=06SqLUw69LOK1N8rhDzWMvQa+zBZdzkTUhnC6gITh+o=; b=arfUQc2B0n69s6dIY2z4S3Vi66 8QfHoXZciB3BcyOqazC7v9hcLOl+9VOsT/sLcgYAy9eVJnQfSZe/WaUoZ8uy2HjqaBCV2Z+f/jLVH WR/xceWwChZpaNN9oMxn5Gr2eKstLrX2DwYy290yQbpBFTFhz1yvtzhBdwVNbwNlgNMWKYJHlwMjS k5IN76NHA+kyipRWWJrQwdMa+8ZHSR+kDqOHWplAMz7hGCi6lZWGKBrAfaOA2wx2eENF5ei3AGO0Z G4MDkeL4GQZ/2NqAbWRcE7T/aYZ7SoBASDPLtItbgFubxX9rKORSFKVNKOOcRmv2S9ncIsWPD0YeW HiAOqQYg==; Received: from authenticated-user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <maxy@debian.org>) id 1x3HMi-000v18-15 for submit@bugs.debian.org; Sun, 06 Sep 2026 18:13:16 +0000 Date: Sun, 6 Sep 2026 20:13:15 +0200 From: Maximiliano Curia <maxy@debian.org> To: submit@bugs.debian.org Subject: python-skbio: FTBFS against python 3.15rc2 Message-ID: <ap2tOyCfyd-31qk3@hecuba.gnuservers.com.ar> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="ZUmjth5SNflhaRHK" Content-Disposition: inline X-Debian-User: maxy Delivered-To: submit@bugs.debian.org --ZUmjth5SNflhaRHK Content-Type: text/plain; charset=us-ascii; format=flowed Content-Disposition: inline Package: src:python-skbio Version: 0.7.3-1 User: debian-python@lists.debian.org Usertags: python3.15 Tags: patch, ftbfs, forky, sid Severity: important Hi! While rebuilding the python related packages against the Python 3.15rc2 version we found that python-skbio fails to build from source [1]. The error is: > super(CompressedMixin, self).__init__(*args, **kwargs) E io.UnsupportedOperation: File or stream is not readable. It seems that its open in write only instead of read only as the test expects, I've created a patch that sets the explicit mode and solves the problem. I applied the fix in the sandbox [2] to be able to build the packages that depend on python-skbio, please consider applying the patch to support the upcoming 3.15 version. Setting the severity to important for now. Once Python 3.15 is released, it will be added to python3-defaults and this bug will become release critical. Happy hacking, [1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4462291/ [2]: https://debusine.debian.net/debian/r-python-python3.15/ -- "Can you imagine what I would do if I could do all I can?" -- Sun Tzu Saludos /\/\ /\ >< `/ --ZUmjth5SNflhaRHK Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename=fix-gzip-reader-mode.patch Description: Explicitly specify mode="rb" in GzipCompressor.get_reader GzipFile without explicit mode defaults to fileobj.mode (e.g. 'w+b' for temporary files), causing it to open for writing instead of reading. Forwarded: not-needed --- a/skbio/io/_iosources.py +++ b/skbio/io/_iosources.py @@ -215,7 +215,7 @@ class GzipCompressor(Compressor): return self.file.peek(2)[:2] == b"\x1f\x8b" def get_reader(self): - return gzip.GzipFile(fileobj=self.file) + return gzip.GzipFile(fileobj=self.file, mode="rb") def get_writer(self): return gzip.GzipFile( --ZUmjth5SNflhaRHK-- ]