Your message dated Thu, 16 Oct 2025 20:41:36 +0000
with message-id <[email protected]>
and subject line Bug#1117022: fixed in ncbi-blast+ 2.17.0+ds-3
has caused the Debian Bug report #1117022,
regarding ncbi-blast+ FTBFS on armhf
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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--
1117022: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1117022
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-blast+
Version: 2.17.0+ds-1
Severity: serious
Tags: ftbfs patch
X-Debbugs-Cc: Aaron M. Ucko <[email protected]>
https://buildd.debian.org/status/logs.php?pkg=ncbi-blast%2B&arch=armhf
...
cc1: error: ‘-mfloat-abi=hard’: selected architecture lacks an FPU
make[5]: ***
[/build/reproducible-path/ncbi-blast+-2.17.0+ds/c++/BUILD/build/Makefile.rules:111:
crc32.o] Error 1
...
/usr/bin/gcc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread
-fopenmp -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/ncbi-blast+-2.17.0+ds=.
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fPIC
-march=armv8-a+crc -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-D_TIME_BITS=64 -D_FORTIFY_SOURCE=2 -D_MT -D_REENTRANT -D_THREAD_SAFE
-I/build/reproducible-path/ncbi-blast+-2.17.0+ds/c++/BUILD/inc
-I/build/reproducible-path/ncbi-blast+-2.17.0+ds/c++/include
-I/build/reproducible-path/ncbi-blast+-2.17.0+ds/c++/include/util/compress/zlib_cloudflare
/build/reproducible-path/ncbi-blast+-2.17.0+ds/c++/src/util/compress/zlib_cloudflare/crc32.c
-o crc32.o
...
This is fixed with the attached patch.
In a related note:
ncbi-blast+ (2.17.0+ds-2) unstable; urgency=medium
* debian/control:
- Additionally build-depend on libsimde-dev.
- Require CRC support on ARM per upstream.
* debian/patches/zcf-simde-crc32c (new): Replace Cloudflare deflate.c's
fallbackless architecture-dependent code with a SIMDE invocation that
amounts to the same thing on supported architectures and to a portable
fallback elsewhere.
-- Aaron M. Ucko <[email protected]> Wed, 01 Oct 2025 14:43:25 -0400
The SIMDE invocation replaces the direct usage of CRC,
which makes the armv8crc-support dependency unnecessary.
Depending on armhf on what is higher even than the arm64
baseline would make little sense in any case.
Description: Don't use -march=armv8-a+crc on arm
Author: Adrian Bunk <[email protected]>
---
ncbi-blast+-2.17.0+ds.orig/c++/src/util/compress/zlib_cloudflare/Makefile.zlib_cf.lib.unix
+++
ncbi-blast+-2.17.0+ds/c++/src/util/compress/zlib_cloudflare/Makefile.zlib_cf.lib.unix
@@ -1,7 +1,7 @@
# $Id: Makefile.zlib_cf.lib.unix 677587 2024-01-18 20:07:53Z ivanov $
-ifneq "" "$(findstring --arm,$(signature))$(findstring --aarch64,$(signature))"
- crc32.o: CFLAGS += -march=armv8-a+crc
- deflate.o: CFLAGS += -march=armv8-a+crc
-endif
+#ifneq "" "$(findstring --arm,$(signature))$(findstring
--aarch64,$(signature))"
+# crc32.o: CFLAGS += -march=armv8-a+crc
+# deflate.o: CFLAGS += -march=armv8-a+crc
+#endif
--- End Message ---
--- Begin Message ---
Source: ncbi-blast+
Source-Version: 2.17.0+ds-3
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ncbi-blast+, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-blast+ package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 16 Oct 2025 16:15:12 -0400
Source: ncbi-blast+
Architecture: source
Version: 2.17.0+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1117022 1117023
Changes:
ncbi-blast+ (2.17.0+ds-3) unstable; urgency=medium
.
* debian/control: Restrict armv8crc-support dependency to arm64.
* debian/patches/support_x32: Slightly broaden configure(.ac)'s VDB
allow-list. (Closes: #1117023.)
* debian/patches/zcf-simde-crc32c: Leave CFLAGS alone on 32-bit ARM;
adjustments aren't actually worthwhile there and would have needed to
go further on armhf, on which (at least under GCC) ARMv8 targets
additionally need +simd. (Closes: #1117022.)
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