[Debian-med-packaging] Bug#1114069: blimps: FTBFS: blksort.c:228:19: error: too many arguments to function 'read_config'; expected 0, have 3

[Sebastien Bacher]

Source: blimps
Followup-For: Bug #1114069
X-Debbugs-Cc: seb128 at ubuntu.com
Control: tags -1 ftbfs

Control: tags -1 + patch
Control: user ubuntu-devel at lists.ubuntu.com
Control: usertags -1 + origin-ubuntu stonking ubuntu-patch

Hi,

We hit this in Ubuntu (gcc-15 15.3) and fixed it as below; the attached
changes build fine, and sift builds against the result.

There are two parts to it:

1. The K&R code doesn't build in C23 mode (gcc-15's default), so build with
   -std=gnu17 (debian-rules.diff):

     -export DEB_CFLAGS_MAINT_APPEND=-Wno-error=implicit-int
     +export DEB_CFLAGS_MAINT_APPEND=-Wno-error=implicit-int -std=gnu17

2. That alone isn't enough, because protomat/Makefile.Linux hardcodes
   "CFLAGS = -Wall -O2 -c" and ignores the DEBCFLAGS/DEBLDFLAGS that the
   top-level Makefile passes (so the protomat tools were also built without
   the hardening flags). protomat-honour-build-flags.patch makes it use them.

   With the hardening flags, -Werror=format-security then catches a real
   issue: extract_seqs() writes sequence data with fprintf(fout, line), i.e.
   the data is used as a format string. protomat-format-security.patch
   switches that (and the same pattern in universa.c) to fputs().

The binary packages' contents are unchanged (the protomat tools are only
built, not shipped).

Ubuntu upload: blimps 3.9+ds-4ubuntu1.

Thanks,
Sebastien Bacher



-- System Information:
Debian Release: forky/sid
  APT prefers resolute-updates
  APT policy: (500, 'resolute-updates'), (500, 'resolute-security'), (500, 'resolute'), (100, 'resolute-backports')
Architecture: amd64 (x86_64)

Kernel: Linux 7.0.0-38-generic (SMP w/16 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
--- a/debian/rules
+++ b/debian/rules
@@ -4,8 +4,8 @@
 # export DH_VERBOSE=1
 
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-# Workaround build failures with gcc-14.
-export DEB_CFLAGS_MAINT_APPEND=-Wno-error=implicit-int
+# Workaround build failures with gcc-14 and gcc-15 (C23 default, K&R code).
+export DEB_CFLAGS_MAINT_APPEND=-Wno-error=implicit-int -std=gnu17
 
 include /usr/share/dpkg/default.mk
 
-------------- next part --------------
Description: Build protomat tools with the build flags passed from the top Makefile
 protomat/Makefile.Linux hardcodes "CFLAGS = -Wall -O2 -c", so the tools
 (blksort, getblock, ...) were built without dpkg-buildflags (hardening,
 -std=gnu17 to cope with gcc-15's C23 default, ...). Use DEBCFLAGS and
 DEBLDFLAGS, which the top-level Makefile already passes, as is done for the
 blimps directory.
Author: Sebastien Bacher <seb128 at ubuntu.com>
Forwarded: https://bugs.debian.org/1114069
Last-Update: 2026-10-09

--- a/protomat/Makefile.Linux
+++ b/protomat/Makefile.Linux
@@ -2,8 +2,8 @@
 #   Type "make install" to compile all programs and move them to ../bin
 #   Type  "make blksort" to compile blksort program 
 CC = gcc
-CFLAGS = -Wall -O2 -c
-LDFLAGS = -lm -o
+CFLAGS = $(DEBCFLAGS) -Wall -O2 -c
+LDFLAGS = $(DEBLDFLAGS) -lm -o
 RM = /bin/rm -f
 MV = /bin/mv -f
 CP = cp -af
-------------- next part --------------
Description: Don't use sequence data as a printf format string
 extract_seqs() wrote sequence lines with fprintf(fout, line), which
 misbehaves if the data contains '%' and fails to build with
 -Werror=format-security once protomat honours the build flags. Use fputs().
Author: Sebastien Bacher <seb128 at ubuntu.com>
Forwarded: https://bugs.debian.org/1114069
Last-Update: 2026-10-09

--- a/protomat/motmisc.c
+++ b/protomat/motmisc.c
@@ -835,7 +835,7 @@ char *pros;
                           if (strpbrk(&line[dbs[db]->seq_offset],
                               "ARNDCQEGHILKMFPSTWYVBZXactg") != NULL)
                           {
-		             if (out) fprintf(fout, &line[dbs[db]->seq_offset]);
+		             if (out) fputs(&line[dbs[db]->seq_offset], fout);
                              for (i=dbs[db]->seq_offset; i<strlen(line); i++)
                                if (isalpha(line[i])) id->len = id->len + 1;
                           }
--- a/protomat/universa.c
+++ b/protomat/universa.c
@@ -204,7 +204,7 @@ int short_title;
 	    {
                for (i=0; i<strlen(line); i++)     /* change CR to space */
                   if (line[i] == CR)  line[i] = ' ';
-	       fprintf(fout, &line[dbs[db]->seq_offset]);
+	       fputs(&line[dbs[db]->seq_offset], fout);
 	    }  /*  end of sequence */
 /*            if (!short_title) fprintf(fout, "\n");   was "*\n" */
 	 }  /*  end of start of entry */