Bug#1120351: biosquid: please make the build reproducible

[Chris Lamb]

Source: biosquid
Version: 1.9g+cvs20050121-15.1
Severity: wishlist
Tags: patch
User: reproducible-builds at lists.alioth.debian.org
Usertags: nocheck
X-Debbugs-Cc: reproducible-bugs at lists.alioth.debian.org

Hi,

Whilst working on the Reproducible Builds effort [0], we noticed that
biosquid could not be built reproducibly.

This is because the package varies depending (I think!) on whether the
tests are run or not:

│ │ │ │ @@ -46,23 +46,23 @@
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     3271 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Formats/stockholm.1
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    21572 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Formats/stockholm.2
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    16663 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Formats/swissprot
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1000 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/00README
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1802 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/Makefile
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1821 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/Makefile.in
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      921 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/bug-1-sfetch-paths
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      921 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/bug-1-sfetch-paths
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      286 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/exercises.sqc
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1898 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/iospeed_main.c
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      673 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/rndspeed_main.c
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      710 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/sqdconfig_main.c
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      865 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/testsuite.pm
│ │ │ │  -rwxr-xr-x   0 root         (0) root         (0)     1572 2006-07-30 21:39:11.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/translate-test.pl
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      370 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-afetch
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      654 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-alistat
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)     1174 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-seqstat
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      336 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-sfetch
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      199 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-shuffle
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      542 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-sindex
│ │ │ │ --rwxr-xr-x   0 root         (0) root         (0)      663 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-sreformat
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      370 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-afetch
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      654 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-alistat
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)     1174 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-seqstat
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      336 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-sfetch
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      199 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-shuffle
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      542 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-sindex
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)      663 2024-02-28 18:29:54.000000 ./usr/share/doc/libsquid-dev/examples/Testsuite/x-base-sreformat


Patch attached that normalises the permissions of these examples.

 [0] https://reproducible-builds.org/


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
-------------- next part --------------
--- a/debian/rules	2025-11-07 14:41:11.757255978 -0800
--- b/debian/rules	2025-11-07 14:51:21.415104610 -0800
@@ -53,6 +53,7 @@
 	done
 
 override_dh_installexamples:
+	chmod 644 Testsuite/*
 	dh_installexamples
 	cd $(CURDIR)/debian/biosquid-dev/usr/share/doc/biosquid-dev/examples/Testsuite; make clean
 	sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(CURDIR)/debian/$(LIBNAME)-dev/usr/share/doc/$(LIBNAME)-dev/examples/Formats/*.pl